Starting phenix.real_space_refine on Tue Aug 4 12:52:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kko_62394/08_2026/9kko_62394.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kko_62394/08_2026/9kko_62394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kko_62394/08_2026/9kko_62394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kko_62394/08_2026/9kko_62394.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kko_62394/08_2026/9kko_62394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kko_62394/08_2026/9kko_62394.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.067 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 17 5.16 5 C 2007 2.51 5 N 491 2.21 5 O 520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3035 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3035 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 27, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 0.62, per 1000 atoms: 0.20 Number of scatterers: 3035 At special positions: 0 Unit cell: (70.832, 65.24, 76.424, 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 17 16.00 O 520 8.00 N 491 7.00 C 2007 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: 0.15 Conformation dependent library (CDL) restraints added in 69.4 milliseconds 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 90.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 25 through 53 removed outlier: 3.848A pdb=" N ILE A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.508A pdb=" N ILE A 61 " --> pdb=" O PRO A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 148 removed outlier: 4.712A pdb=" N LYS A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ALA A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 140 - end of helix Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 151 through 171 Processing helix chain 'A' and resid 174 through 204 removed outlier: 4.606A pdb=" N THR A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 227 removed outlier: 3.843A pdb=" N ARG A 212 " --> pdb=" O PRO A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 removed outlier: 4.035A pdb=" N PHE A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 264 Processing helix chain 'A' and resid 267 through 274 Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 288 through 320 Proline residue: A 304 - end of helix removed outlier: 3.826A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Proline residue: A 310 - end of helix removed outlier: 4.629A pdb=" N ALA A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.712A pdb=" N GLY A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 374 Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 379 through 413 removed outlier: 3.574A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'A' and resid 417 through 447 removed outlier: 3.889A pdb=" N ALA A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Proline residue: A 436 - end of helix removed outlier: 5.719A pdb=" N GLY A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N HIS A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 467 removed outlier: 3.732A pdb=" N ALA A 463 " --> pdb=" O ASN A 459 " (cutoff:3.500A) Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 471 through 475 250 hydrogen bonds defined for protein. 738 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: 0.44 Time building geometry restraints manager: 0.20 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: 938 1.34 - 1.46: 468 1.46 - 1.57: 1677 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 3111 Sorted by residual: bond pdb=" CA SER A 222 " pdb=" C SER A 222 " ideal model delta sigma weight residual 1.524 1.503 0.021 1.24e-02 6.50e+03 2.90e+00 bond pdb=" C ILE A 303 " pdb=" O ILE A 303 " ideal model delta sigma weight residual 1.242 1.229 0.013 8.60e-03 1.35e+04 2.41e+00 bond pdb=" C VAL A 438 " pdb=" O VAL A 438 " ideal model delta sigma weight residual 1.241 1.228 0.013 1.06e-02 8.90e+03 1.56e+00 bond pdb=" CA LEU A 460 " pdb=" C LEU A 460 " ideal model delta sigma weight residual 1.524 1.508 0.016 1.27e-02 6.20e+03 1.53e+00 bond pdb=" CA ALA A 369 " pdb=" C ALA A 369 " ideal model delta sigma weight residual 1.524 1.509 0.015 1.27e-02 6.20e+03 1.33e+00 ... (remaining 3106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 4093 1.47 - 2.93: 119 2.93 - 4.40: 27 4.40 - 5.86: 16 5.86 - 7.33: 2 Bond angle restraints: 4257 Sorted by residual: angle pdb=" CA ILE A 303 " pdb=" C ILE A 303 " pdb=" N PRO A 304 " ideal model delta sigma weight residual 120.83 117.30 3.53 6.10e-01 2.69e+00 3.35e+01 angle pdb=" C VAL A 438 " pdb=" CA VAL A 438 " pdb=" CB VAL A 438 " ideal model delta sigma weight residual 110.88 106.83 4.05 1.09e+00 8.42e-01 1.38e+01 angle pdb=" C ILE A 303 " pdb=" CA ILE A 303 " pdb=" CB ILE A 303 " ideal model delta sigma weight residual 114.00 109.40 4.60 1.31e+00 5.83e-01 1.23e+01 angle pdb=" O ILE A 303 " pdb=" C ILE A 303 " pdb=" N PRO A 304 " ideal model delta sigma weight residual 120.42 122.39 -1.97 6.40e-01 2.44e+00 9.51e+00 angle pdb=" C GLU A 206 " pdb=" N GLU A 207 " pdb=" CA GLU A 207 " ideal model delta sigma weight residual 120.97 124.92 -3.95 1.48e+00 4.57e-01 7.11e+00 ... (remaining 4252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.79: 1622 14.79 - 29.57: 170 29.57 - 44.35: 30 44.35 - 59.14: 13 59.14 - 73.92: 2 Dihedral angle restraints: 1837 sinusoidal: 667 harmonic: 1170 Sorted by residual: dihedral pdb=" CA PHE A 191 " pdb=" C PHE A 191 " pdb=" N ALA A 192 " pdb=" CA ALA A 192 " ideal model delta harmonic sigma weight residual -180.00 -163.18 -16.82 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ASN A 459 " pdb=" CB ASN A 459 " pdb=" CG ASN A 459 " pdb=" OD1 ASN A 459 " ideal model delta sinusoidal sigma weight residual -90.00 -163.92 73.92 2 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA TYR A 352 " pdb=" C TYR A 352 " pdb=" N PRO A 353 " pdb=" CA PRO A 353 " ideal model delta harmonic sigma weight residual -180.00 -164.21 -15.79 0 5.00e+00 4.00e-02 9.97e+00 ... (remaining 1834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 287 0.023 - 0.046: 112 0.046 - 0.068: 63 0.068 - 0.091: 32 0.091 - 0.114: 22 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA PRO A 353 " pdb=" N PRO A 353 " pdb=" C PRO A 353 " pdb=" CB PRO A 353 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.25e-01 chirality pdb=" CA PRO A 58 " pdb=" N PRO A 58 " pdb=" C PRO A 58 " pdb=" CB PRO A 58 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.05e-01 chirality pdb=" CA VAL A 278 " pdb=" N VAL A 278 " pdb=" C VAL A 278 " pdb=" CB VAL A 278 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.10 2.00e-01 2.50e+01 2.74e-01 ... (remaining 513 not shown) Planarity restraints: 530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 27 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 28 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 28 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 28 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 229 " -0.023 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 230 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 228 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO A 229 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " 0.018 5.00e-02 4.00e+02 ... (remaining 527 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 965 2.82 - 3.34: 3208 3.34 - 3.86: 5259 3.86 - 4.38: 5923 4.38 - 4.90: 9873 Nonbonded interactions: 25228 Sorted by model distance: nonbonded pdb=" OD2 ASP A 59 " pdb=" NH2 ARG A 114 " model vdw 2.302 3.120 nonbonded pdb=" OE2 GLU A 207 " pdb=" OG SER A 211 " model vdw 2.304 3.040 nonbonded pdb=" O GLY A 186 " pdb=" OG SER A 189 " model vdw 2.322 3.040 nonbonded pdb=" OD1 ASP A 174 " pdb=" N TYR A 175 " model vdw 2.348 3.120 nonbonded pdb=" OD1 ASP A 398 " pdb=" OH TYR A 428 " model vdw 2.370 3.040 ... (remaining 25223 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: 0.600 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.660 Find NCS groups from input model: 0.020 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.004 0.033 3111 Z= 0.214 Angle : 0.678 7.326 4257 Z= 0.397 Chirality : 0.039 0.114 516 Planarity : 0.005 0.039 530 Dihedral : 13.048 73.923 1085 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % 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 are not related in a simple way. whole: -1.71 (0.38), residues: 400 helix: -0.53 (0.26), residues: 332 sheet: None (None), residues: 0 loop : -3.59 (0.61), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 30 TYR 0.009 0.001 TYR A 352 PHE 0.007 0.001 PHE A 392 TRP 0.002 0.000 TRP A 315 HIS 0.004 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.21 ( 3111) covalent geometry : angle 0.67770 / 0.40 ( 4257) hydrogen bonds : bond 0.14241 / 9.60 ( 250) hydrogen bonds : angle 6.21539 / 4.37 ( 738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.077 Fit side-chains REVERT: A 134 LEU cc_start: 0.8869 (tp) cc_final: 0.8661 (tt) REVERT: A 199 MET cc_start: 0.8690 (ttm) cc_final: 0.8343 (ttm) REVERT: A 264 LYS cc_start: 0.8795 (mttt) cc_final: 0.8529 (mttm) REVERT: A 284 ARG cc_start: 0.8521 (mmt90) cc_final: 0.8057 (mtp85) REVERT: A 317 LYS cc_start: 0.8182 (tttt) cc_final: 0.7718 (ttmt) REVERT: A 326 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7371 (mt-10) REVERT: A 380 PHE cc_start: 0.8199 (t80) cc_final: 0.7674 (t80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0582 time to fit residues: 5.5971 Evaluate side-chains 57 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.095180 restraints weight = 4517.448| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.27 r_work: 0.3114 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3111 Z= 0.149 Angle : 0.654 7.463 4257 Z= 0.313 Chirality : 0.042 0.181 516 Planarity : 0.005 0.040 530 Dihedral : 4.088 17.915 435 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.11 % Allowed : 12.34 % Favored : 83.54 % 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 are not related in a simple way. whole: 0.58 (0.42), residues: 400 helix: 0.99 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.50 (0.67), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 30 TYR 0.034 0.002 TYR A 50 PHE 0.009 0.001 PHE A 392 TRP 0.006 0.001 TRP A 325 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 3111) covalent geometry : angle 0.65444 / 0.31 ( 4257) hydrogen bonds : bond 0.04161 / 2.86 ( 250) hydrogen bonds : angle 4.46369 / 3.16 ( 738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.110 Fit side-chains REVERT: A 50 TYR cc_start: 0.8479 (m-10) cc_final: 0.8182 (m-10) REVERT: A 189 SER cc_start: 0.8500 (p) cc_final: 0.7858 (p) REVERT: A 264 LYS cc_start: 0.8746 (mttt) cc_final: 0.8470 (mttm) REVERT: A 284 ARG cc_start: 0.8806 (mmt90) cc_final: 0.8289 (mtp85) REVERT: A 317 LYS cc_start: 0.8220 (tttt) cc_final: 0.7768 (ttmt) REVERT: A 326 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8097 (mt-10) REVERT: A 380 PHE cc_start: 0.8198 (t80) cc_final: 0.7850 (t80) REVERT: A 470 ARG cc_start: 0.8281 (ptt-90) cc_final: 0.7994 (ptt90) outliers start: 13 outliers final: 9 residues processed: 84 average time/residue: 0.0608 time to fit residues: 6.3149 Evaluate side-chains 72 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 468 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.096279 restraints weight = 4518.160| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.27 r_work: 0.3124 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3111 Z= 0.143 Angle : 0.641 7.408 4257 Z= 0.304 Chirality : 0.041 0.124 516 Planarity : 0.005 0.037 530 Dihedral : 3.996 17.366 435 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 5.38 % Allowed : 14.56 % Favored : 80.06 % 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 are not related in a simple way. whole: 1.18 (0.43), residues: 400 helix: 1.40 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.24 (0.69), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 114 TYR 0.022 0.002 TYR A 50 PHE 0.008 0.001 PHE A 392 TRP 0.005 0.001 TRP A 315 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 3111) covalent geometry : angle 0.64052 / 0.30 ( 4257) hydrogen bonds : bond 0.03800 / 2.64 ( 250) hydrogen bonds : angle 4.28439 / 3.04 ( 738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.069 Fit side-chains REVERT: A 50 TYR cc_start: 0.8397 (m-10) cc_final: 0.8162 (m-10) REVERT: A 189 SER cc_start: 0.8524 (p) cc_final: 0.8145 (p) REVERT: A 207 GLU cc_start: 0.8155 (tp30) cc_final: 0.7906 (tp30) REVERT: A 264 LYS cc_start: 0.8740 (mttt) cc_final: 0.8448 (mttm) REVERT: A 284 ARG cc_start: 0.8819 (mmt90) cc_final: 0.8250 (mtp85) REVERT: A 317 LYS cc_start: 0.8255 (tttt) cc_final: 0.7761 (ttmt) REVERT: A 324 GLU cc_start: 0.7716 (mt-10) cc_final: 0.6365 (tt0) REVERT: A 326 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8146 (mt-10) REVERT: A 380 PHE cc_start: 0.8031 (t80) cc_final: 0.7610 (t80) REVERT: A 470 ARG cc_start: 0.8243 (ptt-90) cc_final: 0.7913 (ptt90) outliers start: 17 outliers final: 10 residues processed: 82 average time/residue: 0.0506 time to fit residues: 5.0826 Evaluate side-chains 74 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 468 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.097134 restraints weight = 4438.587| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.24 r_work: 0.3140 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3111 Z= 0.131 Angle : 0.629 7.429 4257 Z= 0.296 Chirality : 0.040 0.138 516 Planarity : 0.005 0.036 530 Dihedral : 3.901 17.678 435 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.11 % Allowed : 17.09 % Favored : 78.80 % 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 are not related in a simple way. whole: 1.35 (0.43), residues: 400 helix: 1.51 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.15 (0.69), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.018 0.002 TYR A 50 PHE 0.008 0.001 PHE A 392 TRP 0.004 0.001 TRP A 315 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 3111) covalent geometry : angle 0.62908 / 0.30 ( 4257) hydrogen bonds : bond 0.03535 / 2.45 ( 250) hydrogen bonds : angle 4.12512 / 2.93 ( 738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.068 Fit side-chains REVERT: A 207 GLU cc_start: 0.8111 (tp30) cc_final: 0.7823 (tp30) REVERT: A 264 LYS cc_start: 0.8751 (mttt) cc_final: 0.8550 (mttp) REVERT: A 275 ASN cc_start: 0.8005 (m-40) cc_final: 0.7745 (m-40) REVERT: A 284 ARG cc_start: 0.8796 (mmt90) cc_final: 0.8287 (mtp85) REVERT: A 317 LYS cc_start: 0.8221 (tttt) cc_final: 0.7986 (tttm) REVERT: A 324 GLU cc_start: 0.7706 (mt-10) cc_final: 0.6380 (tt0) REVERT: A 462 TYR cc_start: 0.8978 (t80) cc_final: 0.8604 (t80) REVERT: A 470 ARG cc_start: 0.8222 (ptt-90) cc_final: 0.8017 (ptt90) outliers start: 13 outliers final: 10 residues processed: 81 average time/residue: 0.0390 time to fit residues: 3.9113 Evaluate side-chains 73 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 468 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.118382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097712 restraints weight = 4455.797| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.24 r_work: 0.3138 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3111 Z= 0.141 Angle : 0.649 7.229 4257 Z= 0.305 Chirality : 0.041 0.198 516 Planarity : 0.005 0.037 530 Dihedral : 3.844 17.288 435 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.11 % Allowed : 19.30 % Favored : 76.58 % 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 are not related in a simple way. whole: 1.42 (0.43), residues: 400 helix: 1.55 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.12 (0.68), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.037 0.002 TYR A 50 PHE 0.008 0.001 PHE A 392 TRP 0.004 0.001 TRP A 315 HIS 0.002 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 3111) covalent geometry : angle 0.64896 / 0.31 ( 4257) hydrogen bonds : bond 0.03518 / 2.43 ( 250) hydrogen bonds : angle 4.12022 / 2.93 ( 738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.064 Fit side-chains REVERT: A 207 GLU cc_start: 0.8091 (tp30) cc_final: 0.7767 (tp30) REVERT: A 264 LYS cc_start: 0.8769 (mttt) cc_final: 0.8549 (mttp) REVERT: A 275 ASN cc_start: 0.8026 (m-40) cc_final: 0.7778 (m-40) REVERT: A 284 ARG cc_start: 0.8774 (mmt90) cc_final: 0.8251 (mtp85) REVERT: A 317 LYS cc_start: 0.8256 (tttt) cc_final: 0.8031 (tttm) REVERT: A 324 GLU cc_start: 0.7717 (mt-10) cc_final: 0.6414 (tt0) REVERT: A 462 TYR cc_start: 0.9006 (t80) cc_final: 0.8688 (t80) outliers start: 13 outliers final: 12 residues processed: 79 average time/residue: 0.0379 time to fit residues: 3.7946 Evaluate side-chains 69 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 468 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.117978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095929 restraints weight = 4243.214| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.33 r_work: 0.3064 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3111 Z= 0.131 Angle : 0.634 7.142 4257 Z= 0.304 Chirality : 0.040 0.115 516 Planarity : 0.005 0.037 530 Dihedral : 3.818 18.710 435 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 5.38 % Allowed : 20.25 % Favored : 74.37 % 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 are not related in a simple way. whole: 1.52 (0.43), residues: 400 helix: 1.62 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.06 (0.67), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.031 0.002 TYR A 50 PHE 0.008 0.001 PHE A 392 TRP 0.005 0.001 TRP A 315 HIS 0.002 0.001 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 3111) covalent geometry : angle 0.63373 / 0.30 ( 4257) hydrogen bonds : bond 0.03363 / 2.30 ( 250) hydrogen bonds : angle 4.03332 / 2.86 ( 738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.064 Fit side-chains REVERT: A 237 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8470 (mm-30) REVERT: A 264 LYS cc_start: 0.8612 (mttt) cc_final: 0.8398 (mttp) REVERT: A 275 ASN cc_start: 0.7943 (m-40) cc_final: 0.7712 (m-40) REVERT: A 284 ARG cc_start: 0.8765 (mmt90) cc_final: 0.8212 (mtp85) REVERT: A 324 GLU cc_start: 0.7640 (mt-10) cc_final: 0.6299 (tt0) REVERT: A 355 LEU cc_start: 0.8576 (mt) cc_final: 0.7863 (mp) REVERT: A 462 TYR cc_start: 0.8906 (t80) cc_final: 0.8591 (t80) outliers start: 17 outliers final: 13 residues processed: 78 average time/residue: 0.0364 time to fit residues: 3.6090 Evaluate side-chains 74 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 467 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.118502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.096422 restraints weight = 4353.560| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.36 r_work: 0.3077 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3111 Z= 0.139 Angle : 0.673 7.986 4257 Z= 0.313 Chirality : 0.041 0.192 516 Planarity : 0.005 0.037 530 Dihedral : 3.842 18.308 435 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 5.06 % Allowed : 21.52 % Favored : 73.42 % 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 are not related in a simple way. whole: 1.52 (0.43), residues: 400 helix: 1.62 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.06 (0.68), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.029 0.002 TYR A 50 PHE 0.008 0.001 PHE A 392 TRP 0.003 0.000 TRP A 315 HIS 0.002 0.001 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 3111) covalent geometry : angle 0.67317 / 0.31 ( 4257) hydrogen bonds : bond 0.03397 / 2.37 ( 250) hydrogen bonds : angle 4.13125 / 2.93 ( 738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.100 Fit side-chains REVERT: A 264 LYS cc_start: 0.8607 (mttt) cc_final: 0.8387 (mttp) REVERT: A 275 ASN cc_start: 0.7981 (m-40) cc_final: 0.7762 (m-40) REVERT: A 284 ARG cc_start: 0.8767 (mmt90) cc_final: 0.8213 (mtp85) REVERT: A 324 GLU cc_start: 0.7639 (mt-10) cc_final: 0.6322 (tt0) REVERT: A 355 LEU cc_start: 0.8559 (mt) cc_final: 0.7650 (mp) REVERT: A 462 TYR cc_start: 0.8921 (t80) cc_final: 0.8620 (t80) REVERT: A 470 ARG cc_start: 0.8250 (ptt90) cc_final: 0.7924 (ptt90) outliers start: 16 outliers final: 14 residues processed: 71 average time/residue: 0.0495 time to fit residues: 4.4109 Evaluate side-chains 72 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 468 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.119325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.096861 restraints weight = 4454.579| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.42 r_work: 0.3085 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3111 Z= 0.128 Angle : 0.645 7.003 4257 Z= 0.303 Chirality : 0.040 0.142 516 Planarity : 0.005 0.037 530 Dihedral : 3.774 17.863 435 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.75 % Allowed : 20.89 % Favored : 74.37 % 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 are not related in a simple way. whole: 1.66 (0.43), residues: 400 helix: 1.71 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.98 (0.67), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 470 TYR 0.027 0.002 TYR A 50 PHE 0.008 0.001 PHE A 392 TRP 0.002 0.000 TRP A 315 HIS 0.002 0.001 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 3111) covalent geometry : angle 0.64454 / 0.30 ( 4257) hydrogen bonds : bond 0.03253 / 2.23 ( 250) hydrogen bonds : angle 4.05646 / 2.87 ( 738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.077 Fit side-chains REVERT: A 237 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8416 (mm-30) REVERT: A 264 LYS cc_start: 0.8608 (mttt) cc_final: 0.8387 (mttp) REVERT: A 275 ASN cc_start: 0.7968 (m-40) cc_final: 0.7762 (m-40) REVERT: A 284 ARG cc_start: 0.8747 (mmt90) cc_final: 0.8195 (mtp85) REVERT: A 324 GLU cc_start: 0.7623 (mt-10) cc_final: 0.6303 (tt0) REVERT: A 355 LEU cc_start: 0.8574 (mt) cc_final: 0.7627 (mp) REVERT: A 462 TYR cc_start: 0.8921 (t80) cc_final: 0.8617 (t80) REVERT: A 470 ARG cc_start: 0.8258 (ptt90) cc_final: 0.7948 (ptt90) outliers start: 15 outliers final: 13 residues processed: 81 average time/residue: 0.0468 time to fit residues: 4.7915 Evaluate side-chains 79 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 468 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095423 restraints weight = 4432.146| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.38 r_work: 0.3066 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3111 Z= 0.143 Angle : 0.664 7.074 4257 Z= 0.310 Chirality : 0.042 0.230 516 Planarity : 0.005 0.037 530 Dihedral : 3.755 17.376 435 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.70 % Allowed : 20.89 % Favored : 73.42 % 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 are not related in a simple way. whole: 1.72 (0.43), residues: 400 helix: 1.75 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.91 (0.67), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.023 0.002 TYR A 50 PHE 0.008 0.001 PHE A 392 TRP 0.002 0.000 TRP A 331 HIS 0.002 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.14 ( 3111) covalent geometry : angle 0.66436 / 0.31 ( 4257) hydrogen bonds : bond 0.03394 / 2.33 ( 250) hydrogen bonds : angle 4.10032 / 2.91 ( 738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.078 Fit side-chains REVERT: A 284 ARG cc_start: 0.8745 (mmt90) cc_final: 0.8190 (mtp85) REVERT: A 324 GLU cc_start: 0.7628 (mt-10) cc_final: 0.6315 (tt0) REVERT: A 355 LEU cc_start: 0.8606 (mt) cc_final: 0.7657 (mp) REVERT: A 462 TYR cc_start: 0.8956 (t80) cc_final: 0.8693 (t80) outliers start: 18 outliers final: 16 residues processed: 78 average time/residue: 0.0457 time to fit residues: 4.4989 Evaluate side-chains 76 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.095239 restraints weight = 4329.433| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.35 r_work: 0.3064 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3111 Z= 0.151 Angle : 0.674 7.075 4257 Z= 0.317 Chirality : 0.042 0.198 516 Planarity : 0.005 0.037 530 Dihedral : 3.776 17.425 435 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.75 % Allowed : 23.42 % Favored : 71.84 % 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 are not related in a simple way. whole: 1.68 (0.43), residues: 400 helix: 1.71 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.94 (0.67), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.023 0.002 TYR A 50 PHE 0.008 0.001 PHE A 392 TRP 0.001 0.000 TRP A 357 HIS 0.002 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.15 ( 3111) covalent geometry : angle 0.67404 / 0.32 ( 4257) hydrogen bonds : bond 0.03477 / 2.38 ( 250) hydrogen bonds : angle 4.09438 / 2.91 ( 738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.069 Fit side-chains REVERT: A 50 TYR cc_start: 0.7665 (m-10) cc_final: 0.7410 (m-10) REVERT: A 199 MET cc_start: 0.8848 (ttm) cc_final: 0.8611 (ttm) REVERT: A 284 ARG cc_start: 0.8755 (mmt90) cc_final: 0.8195 (mtp85) REVERT: A 324 GLU cc_start: 0.7642 (mt-10) cc_final: 0.6323 (tt0) REVERT: A 462 TYR cc_start: 0.8964 (t80) cc_final: 0.8719 (t80) outliers start: 15 outliers final: 15 residues processed: 74 average time/residue: 0.0475 time to fit residues: 4.4038 Evaluate side-chains 75 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096084 restraints weight = 4331.432| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.37 r_work: 0.3075 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3111 Z= 0.141 Angle : 0.672 7.054 4257 Z= 0.314 Chirality : 0.042 0.185 516 Planarity : 0.005 0.037 530 Dihedral : 3.752 17.550 435 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.75 % Allowed : 23.73 % Favored : 71.52 % 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 are not related in a simple way. whole: 1.79 (0.43), residues: 400 helix: 1.77 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.85 (0.68), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.023 0.002 TYR A 50 PHE 0.022 0.001 PHE A 145 TRP 0.002 0.000 TRP A 357 HIS 0.002 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 3111) covalent geometry : angle 0.67169 / 0.31 ( 4257) hydrogen bonds : bond 0.03406 / 2.33 ( 250) hydrogen bonds : angle 4.06360 / 2.89 ( 738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 761.63 seconds wall clock time: 13 minutes 41.84 seconds (821.84 seconds total)