Starting phenix.real_space_refine on Thu Jul 2 00:03:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jg4_61450/07_2026/9jg4_61450.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jg4_61450/07_2026/9jg4_61450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jg4_61450/07_2026/9jg4_61450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jg4_61450/07_2026/9jg4_61450.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jg4_61450/07_2026/9jg4_61450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jg4_61450/07_2026/9jg4_61450.map" } resolution = 3.02 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= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 Cl 1 4.86 5 C 2905 2.51 5 N 660 2.21 5 O 744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4342 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4333 Classifications: {'peptide': 544} Link IDs: {'PTRANS': 27, 'TRANS': 516} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 8 Ad-hoc single atom residues: {' CL': 1} Classifications: {'water': 8} Link IDs: {None: 7} Chain breaks: 1 Time building chain proxies: 1.13, per 1000 atoms: 0.26 Number of scatterers: 4342 At special positions: 0 Unit cell: (81.03, 64.24, 88.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 32 16.00 O 744 8.00 N 660 7.00 C 2905 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " 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: 0.27 Conformation dependent library (CDL) restraints added in 160.8 milliseconds 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 992 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 79.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 46 through 56 removed outlier: 3.684A pdb=" N GLY A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 4.107A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.582A pdb=" N TYR A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 85 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 106 removed outlier: 3.509A pdb=" N PHE A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.662A pdb=" N ILE A 116 " --> pdb=" O CYS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 138 removed outlier: 4.426A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.245A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'A' and resid 244 through 266 removed outlier: 4.438A pdb=" N PHE A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.751A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 286 Processing helix chain 'A' and resid 287 through 302 removed outlier: 3.984A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.565A pdb=" N SER A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.101A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.733A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.608A pdb=" N ILE A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.647A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 removed outlier: 4.049A pdb=" N LYS A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 443 Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 481 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.938A pdb=" N LEU A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.846A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 581 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 276 hydrogen bonds defined for protein. 819 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: 0.66 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1260 1.34 - 1.46: 1247 1.46 - 1.58: 1923 1.58 - 1.70: 0 1.70 - 1.81: 46 Bond restraints: 4476 Sorted by residual: bond pdb=" C ALA A 55 " pdb=" N GLY A 56 " ideal model delta sigma weight residual 1.319 1.329 -0.011 1.34e-02 5.57e+03 6.19e-01 bond pdb=" CA VAL A 528 " pdb=" C VAL A 528 " ideal model delta sigma weight residual 1.522 1.518 0.005 7.10e-03 1.98e+04 4.15e-01 bond pdb=" C VAL A 447 " pdb=" O VAL A 447 " ideal model delta sigma weight residual 1.236 1.226 0.009 1.47e-02 4.63e+03 4.09e-01 bond pdb=" CA TYR A 374 " pdb=" C TYR A 374 " ideal model delta sigma weight residual 1.522 1.530 -0.008 1.26e-02 6.30e+03 4.02e-01 bond pdb=" C TYR A 374 " pdb=" O TYR A 374 " ideal model delta sigma weight residual 1.244 1.238 0.006 9.80e-03 1.04e+04 3.53e-01 ... (remaining 4471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 5966 1.36 - 2.73: 115 2.73 - 4.09: 17 4.09 - 5.46: 5 5.46 - 6.82: 4 Bond angle restraints: 6107 Sorted by residual: angle pdb=" C GLY A 91 " pdb=" N LEU A 92 " pdb=" CA LEU A 92 " ideal model delta sigma weight residual 121.80 115.41 6.39 2.44e+00 1.68e-01 6.87e+00 angle pdb=" C GLY A 56 " pdb=" N GLY A 57 " pdb=" CA GLY A 57 " ideal model delta sigma weight residual 119.92 121.82 -1.90 9.60e-01 1.09e+00 3.94e+00 angle pdb=" CA LEU A 52 " pdb=" CB LEU A 52 " pdb=" CG LEU A 52 " ideal model delta sigma weight residual 116.30 123.12 -6.82 3.50e+00 8.16e-02 3.80e+00 angle pdb=" CA VAL A 557 " pdb=" C VAL A 557 " pdb=" N PRO A 558 " ideal model delta sigma weight residual 118.88 121.51 -2.63 1.54e+00 4.22e-01 2.92e+00 angle pdb=" C ALA A 373 " pdb=" N TYR A 374 " pdb=" CA TYR A 374 " ideal model delta sigma weight residual 120.09 122.23 -2.14 1.25e+00 6.40e-01 2.92e+00 ... (remaining 6102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 2407 15.88 - 31.76: 89 31.76 - 47.64: 22 47.64 - 63.52: 7 63.52 - 79.39: 3 Dihedral angle restraints: 2528 sinusoidal: 960 harmonic: 1568 Sorted by residual: dihedral pdb=" CA GLY A 91 " pdb=" C GLY A 91 " pdb=" N LEU A 92 " pdb=" CA LEU A 92 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" N GLN A 456 " pdb=" CA GLN A 456 " pdb=" CB GLN A 456 " pdb=" CG GLN A 456 " ideal model delta sinusoidal sigma weight residual -180.00 -124.23 -55.77 3 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" N TYR A 69 " pdb=" CA TYR A 69 " pdb=" CB TYR A 69 " pdb=" CG TYR A 69 " ideal model delta sinusoidal sigma weight residual 60.00 115.69 -55.69 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 2525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 445 0.026 - 0.053: 131 0.053 - 0.079: 70 0.079 - 0.105: 26 0.105 - 0.132: 2 Chirality restraints: 674 Sorted by residual: chirality pdb=" CA LEU A 92 " pdb=" N LEU A 92 " pdb=" C LEU A 92 " pdb=" CB LEU A 92 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA THR A 512 " pdb=" N THR A 512 " pdb=" C THR A 512 " pdb=" CB THR A 512 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.11 2.00e-01 2.50e+01 3.25e-01 chirality pdb=" CA VAL A 59 " pdb=" N VAL A 59 " pdb=" C VAL A 59 " pdb=" CB VAL A 59 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.10 2.00e-01 2.50e+01 2.72e-01 ... (remaining 671 not shown) Planarity restraints: 743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 89 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C GLY A 89 " -0.031 2.00e-02 2.50e+03 pdb=" O GLY A 89 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 90 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 581 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 582 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 582 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 582 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 87 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C LEU A 87 " 0.025 2.00e-02 2.50e+03 pdb=" O LEU A 87 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE A 88 " -0.009 2.00e-02 2.50e+03 ... (remaining 740 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 180 2.73 - 3.27: 4591 3.27 - 3.82: 7544 3.82 - 4.36: 8498 4.36 - 4.90: 15362 Nonbonded interactions: 36175 Sorted by model distance: nonbonded pdb=" O ASP A 459 " pdb=" OG SER A 464 " model vdw 2.188 3.040 nonbonded pdb=" O SER A 311 " pdb=" OG SER A 314 " model vdw 2.328 3.040 nonbonded pdb=" O LEU A 70 " pdb=" ND2 ASN A 74 " model vdw 2.338 3.120 nonbonded pdb=" O TRP A 166 " pdb=" NH1 ARG A 201 " model vdw 2.341 3.120 nonbonded pdb=" OD1 ASN A 63 " pdb=" OG SER A 337 " model vdw 2.354 3.040 ... (remaining 36170 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.850 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4477 Z= 0.103 Angle : 0.496 6.820 6109 Z= 0.286 Chirality : 0.034 0.132 674 Planarity : 0.004 0.038 743 Dihedral : 9.982 79.394 1533 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.85 % Allowed : 3.64 % Favored : 92.51 % 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: -0.70 (0.34), residues: 542 helix: 0.19 (0.26), residues: 367 sheet: None (None), residues: 0 loop : -1.74 (0.45), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 587 TYR 0.008 0.001 TYR A 69 PHE 0.007 0.001 PHE A 338 TRP 0.008 0.001 TRP A 470 HIS 0.001 0.000 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00173 / 0.10 ( 4476) covalent geometry : angle 0.49648 / 0.29 ( 6107) SS BOND : bond 0.00105 / 0.06 ( 1) SS BOND : angle 0.44293 / 0.26 ( 2) hydrogen bonds : bond 0.16176 / 10.19 ( 276) hydrogen bonds : angle 6.58175 / 4.57 ( 819) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.116 Fit side-chains REVERT: A 323 TYR cc_start: 0.7474 (t80) cc_final: 0.7259 (t80) REVERT: A 328 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6983 (tm) REVERT: A 427 ARG cc_start: 0.7365 (mtm180) cc_final: 0.5248 (tpt170) REVERT: A 481 TRP cc_start: 0.8267 (m100) cc_final: 0.8035 (m100) REVERT: A 584 GLU cc_start: 0.3535 (OUTLIER) cc_final: 0.3314 (mt-10) outliers start: 18 outliers final: 1 residues processed: 131 average time/residue: 0.0526 time to fit residues: 9.1025 Evaluate side-chains 88 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 584 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 HIS A 202 ASN A 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.171346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.140614 restraints weight = 5277.432| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.99 r_work: 0.3490 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4477 Z= 0.119 Angle : 0.502 6.074 6109 Z= 0.258 Chirality : 0.038 0.146 674 Planarity : 0.004 0.034 743 Dihedral : 5.208 81.665 598 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.21 % Allowed : 10.28 % Favored : 86.51 % 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: 1.17 (0.36), residues: 542 helix: 1.47 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.87 (0.50), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.011 0.001 TYR A 277 PHE 0.019 0.002 PHE A 96 TRP 0.014 0.001 TRP A 236 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 4476) covalent geometry : angle 0.50171 / 0.26 ( 6107) SS BOND : bond 0.00281 / 0.15 ( 1) SS BOND : angle 0.96890 / 0.54 ( 2) hydrogen bonds : bond 0.03474 / 2.30 ( 276) hydrogen bonds : angle 4.47476 / 3.12 ( 819) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.133 Fit side-chains REVERT: A 69 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.7009 (t80) REVERT: A 311 SER cc_start: 0.7957 (m) cc_final: 0.7749 (p) REVERT: A 328 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7695 (tm) REVERT: A 427 ARG cc_start: 0.7316 (mtm180) cc_final: 0.4843 (tpt170) REVERT: A 432 ILE cc_start: 0.7681 (mt) cc_final: 0.7444 (mt) REVERT: A 584 GLU cc_start: 0.4781 (OUTLIER) cc_final: 0.3947 (mt-10) outliers start: 15 outliers final: 10 residues processed: 90 average time/residue: 0.0444 time to fit residues: 5.6211 Evaluate side-chains 85 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 236 TRP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 584 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 456 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123329 restraints weight = 5319.180| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.02 r_work: 0.3278 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4477 Z= 0.148 Angle : 0.537 7.204 6109 Z= 0.270 Chirality : 0.039 0.144 674 Planarity : 0.004 0.035 743 Dihedral : 5.439 83.733 598 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.21 % Allowed : 11.78 % Favored : 85.01 % 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: 1.22 (0.36), residues: 542 helix: 1.58 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.13 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.021 0.001 TYR A 460 PHE 0.020 0.002 PHE A 95 TRP 0.014 0.002 TRP A 236 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 4476) covalent geometry : angle 0.53640 / 0.27 ( 6107) SS BOND : bond 0.00310 / 0.16 ( 1) SS BOND : angle 1.02718 / 0.58 ( 2) hydrogen bonds : bond 0.03933 / 2.63 ( 276) hydrogen bonds : angle 4.42897 / 3.13 ( 819) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.090 Fit side-chains REVERT: A 176 MET cc_start: 0.7534 (mmm) cc_final: 0.7224 (mmm) REVERT: A 311 SER cc_start: 0.8122 (m) cc_final: 0.7896 (p) REVERT: A 312 LEU cc_start: 0.7273 (tp) cc_final: 0.6887 (mt) REVERT: A 320 TYR cc_start: 0.8795 (t80) cc_final: 0.8544 (t80) REVERT: A 395 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8572 (mp) REVERT: A 427 ARG cc_start: 0.7352 (mtm180) cc_final: 0.4725 (tpt170) REVERT: A 521 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8418 (mt) REVERT: A 577 LYS cc_start: 0.7785 (mmmm) cc_final: 0.7482 (mmtp) REVERT: A 584 GLU cc_start: 0.4886 (OUTLIER) cc_final: 0.3996 (mt-10) outliers start: 15 outliers final: 7 residues processed: 85 average time/residue: 0.0521 time to fit residues: 5.9394 Evaluate side-chains 74 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 584 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 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 = 0.3739 r_free = 0.3739 target = 0.152772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119849 restraints weight = 5302.361| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.02 r_work: 0.3238 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4477 Z= 0.138 Angle : 0.517 7.241 6109 Z= 0.261 Chirality : 0.039 0.144 674 Planarity : 0.004 0.048 743 Dihedral : 5.241 86.497 596 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.00 % Allowed : 12.21 % Favored : 84.80 % 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: 1.20 (0.36), residues: 542 helix: 1.59 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -1.17 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.013 0.001 TYR A 460 PHE 0.017 0.001 PHE A 392 TRP 0.012 0.001 TRP A 236 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 4476) covalent geometry : angle 0.51667 / 0.26 ( 6107) SS BOND : bond 0.00304 / 0.16 ( 1) SS BOND : angle 1.12173 / 0.62 ( 2) hydrogen bonds : bond 0.03645 / 2.43 ( 276) hydrogen bonds : angle 4.43323 / 3.10 ( 819) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.153 Fit side-chains REVERT: A 175 THR cc_start: 0.9038 (p) cc_final: 0.8680 (p) REVERT: A 176 MET cc_start: 0.7563 (mmm) cc_final: 0.7247 (mmm) REVERT: A 312 LEU cc_start: 0.7484 (tp) cc_final: 0.7035 (mt) REVERT: A 320 TYR cc_start: 0.8778 (t80) cc_final: 0.8463 (t80) REVERT: A 358 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7927 (t0) REVERT: A 521 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8445 (mt) REVERT: A 577 LYS cc_start: 0.7847 (mmmm) cc_final: 0.7542 (mmtp) REVERT: A 584 GLU cc_start: 0.5085 (OUTLIER) cc_final: 0.4113 (mt-10) outliers start: 14 outliers final: 10 residues processed: 76 average time/residue: 0.0397 time to fit residues: 4.4072 Evaluate side-chains 77 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 584 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.152018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.118796 restraints weight = 5364.157| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.05 r_work: 0.3223 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4477 Z= 0.127 Angle : 0.508 6.986 6109 Z= 0.254 Chirality : 0.038 0.134 674 Planarity : 0.004 0.043 743 Dihedral : 5.172 86.965 596 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.21 % Allowed : 12.21 % Favored : 84.58 % 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: 1.33 (0.37), residues: 542 helix: 1.70 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -1.14 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 201 TYR 0.014 0.001 TYR A 69 PHE 0.015 0.001 PHE A 95 TRP 0.011 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 4476) covalent geometry : angle 0.50754 / 0.25 ( 6107) SS BOND : bond 0.00283 / 0.15 ( 1) SS BOND : angle 1.02123 / 0.58 ( 2) hydrogen bonds : bond 0.03576 / 2.40 ( 276) hydrogen bonds : angle 4.40695 / 3.07 ( 819) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.136 Fit side-chains REVERT: A 176 MET cc_start: 0.7557 (mmm) cc_final: 0.7243 (mmm) REVERT: A 320 TYR cc_start: 0.8756 (t80) cc_final: 0.8494 (t80) REVERT: A 358 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7892 (t0) REVERT: A 521 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8471 (mt) REVERT: A 577 LYS cc_start: 0.7839 (mmmm) cc_final: 0.7554 (mmtp) REVERT: A 584 GLU cc_start: 0.5120 (OUTLIER) cc_final: 0.4167 (mt-10) outliers start: 15 outliers final: 10 residues processed: 73 average time/residue: 0.0284 time to fit residues: 3.0424 Evaluate side-chains 77 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 584 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.150300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117128 restraints weight = 5442.643| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.05 r_work: 0.3203 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4477 Z= 0.134 Angle : 0.516 7.263 6109 Z= 0.258 Chirality : 0.039 0.135 674 Planarity : 0.004 0.049 743 Dihedral : 5.217 87.906 596 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.64 % Allowed : 11.99 % Favored : 84.37 % 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: 1.36 (0.37), residues: 542 helix: 1.73 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -1.16 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.014 0.001 TYR A 69 PHE 0.016 0.001 PHE A 95 TRP 0.011 0.001 TRP A 470 HIS 0.005 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 4476) covalent geometry : angle 0.51524 / 0.26 ( 6107) SS BOND : bond 0.00265 / 0.14 ( 1) SS BOND : angle 1.08967 / 0.61 ( 2) hydrogen bonds : bond 0.03674 / 2.44 ( 276) hydrogen bonds : angle 4.43413 / 3.09 ( 819) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.111 Fit side-chains REVERT: A 86 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7941 (t80) REVERT: A 236 TRP cc_start: 0.8566 (t60) cc_final: 0.7930 (t60) REVERT: A 320 TYR cc_start: 0.8773 (t80) cc_final: 0.8520 (t80) REVERT: A 358 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7892 (t0) REVERT: A 521 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8501 (mt) REVERT: A 577 LYS cc_start: 0.7860 (mmmm) cc_final: 0.7591 (mmtp) REVERT: A 584 GLU cc_start: 0.5101 (OUTLIER) cc_final: 0.4074 (mt-10) outliers start: 17 outliers final: 9 residues processed: 77 average time/residue: 0.0296 time to fit residues: 3.3595 Evaluate side-chains 76 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 584 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120294 restraints weight = 5388.329| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.95 r_work: 0.3237 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4477 Z= 0.111 Angle : 0.496 6.323 6109 Z= 0.247 Chirality : 0.037 0.131 674 Planarity : 0.004 0.049 743 Dihedral : 5.149 87.464 596 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.00 % Allowed : 13.06 % Favored : 83.94 % 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 (0.37), residues: 542 helix: 1.74 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.95 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 499 TYR 0.012 0.001 TYR A 69 PHE 0.014 0.001 PHE A 191 TRP 0.012 0.001 TRP A 470 HIS 0.006 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 4476) covalent geometry : angle 0.49564 / 0.25 ( 6107) SS BOND : bond 0.00211 / 0.11 ( 1) SS BOND : angle 0.98527 / 0.56 ( 2) hydrogen bonds : bond 0.03412 / 2.26 ( 276) hydrogen bonds : angle 4.35413 / 3.03 ( 819) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.153 Fit side-chains REVERT: A 69 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7855 (t80) REVERT: A 86 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.7938 (t80) REVERT: A 236 TRP cc_start: 0.8518 (t60) cc_final: 0.7914 (t60) REVERT: A 320 TYR cc_start: 0.8794 (t80) cc_final: 0.8591 (t80) REVERT: A 358 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7953 (t0) REVERT: A 432 ILE cc_start: 0.7915 (mt) cc_final: 0.7708 (mt) REVERT: A 521 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8537 (mt) REVERT: A 577 LYS cc_start: 0.7918 (mmmm) cc_final: 0.7673 (mmtp) REVERT: A 584 GLU cc_start: 0.4979 (OUTLIER) cc_final: 0.4047 (mt-10) outliers start: 14 outliers final: 7 residues processed: 78 average time/residue: 0.0436 time to fit residues: 4.9770 Evaluate side-chains 77 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 584 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 42 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.152351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119798 restraints weight = 5411.894| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.96 r_work: 0.3218 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4477 Z= 0.113 Angle : 0.503 6.686 6109 Z= 0.251 Chirality : 0.037 0.131 674 Planarity : 0.004 0.048 743 Dihedral : 5.141 86.756 596 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.78 % Allowed : 13.92 % Favored : 83.30 % 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: 1.57 (0.37), residues: 542 helix: 1.80 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.97 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 240 TYR 0.012 0.001 TYR A 69 PHE 0.014 0.001 PHE A 191 TRP 0.012 0.001 TRP A 470 HIS 0.005 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 4476) covalent geometry : angle 0.50282 / 0.25 ( 6107) SS BOND : bond 0.00206 / 0.11 ( 1) SS BOND : angle 1.01206 / 0.57 ( 2) hydrogen bonds : bond 0.03454 / 2.28 ( 276) hydrogen bonds : angle 4.32187 / 3.01 ( 819) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.161 Fit side-chains REVERT: A 69 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.7792 (t80) REVERT: A 86 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.7970 (t80) REVERT: A 236 TRP cc_start: 0.8509 (t60) cc_final: 0.7913 (t60) REVERT: A 358 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7968 (t0) REVERT: A 521 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8588 (mt) REVERT: A 577 LYS cc_start: 0.7923 (mmmm) cc_final: 0.7681 (mmtp) REVERT: A 584 GLU cc_start: 0.4970 (OUTLIER) cc_final: 0.4093 (mt-10) outliers start: 13 outliers final: 8 residues processed: 75 average time/residue: 0.0415 time to fit residues: 4.5473 Evaluate side-chains 75 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 584 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.151862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119545 restraints weight = 5401.380| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.94 r_work: 0.3217 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4477 Z= 0.120 Angle : 0.523 7.265 6109 Z= 0.263 Chirality : 0.038 0.191 674 Planarity : 0.004 0.049 743 Dihedral : 5.223 86.694 596 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.00 % Allowed : 14.35 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.37), residues: 542 helix: 1.80 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -1.00 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.013 0.001 TYR A 69 PHE 0.015 0.001 PHE A 191 TRP 0.012 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 4476) covalent geometry : angle 0.52014 / 0.26 ( 6107) SS BOND : bond 0.00294 / 0.15 ( 1) SS BOND : angle 2.91870 / 1.54 ( 2) hydrogen bonds : bond 0.03499 / 2.31 ( 276) hydrogen bonds : angle 4.33894 / 3.02 ( 819) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.100 Fit side-chains REVERT: A 69 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.7716 (t80) REVERT: A 86 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.7876 (t80) REVERT: A 176 MET cc_start: 0.7535 (mmm) cc_final: 0.7197 (mmm) REVERT: A 236 TRP cc_start: 0.8505 (t60) cc_final: 0.7857 (t60) REVERT: A 320 TYR cc_start: 0.8759 (t80) cc_final: 0.8340 (t80) REVERT: A 358 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7825 (t0) REVERT: A 421 PHE cc_start: 0.7672 (t80) cc_final: 0.7386 (t80) REVERT: A 504 MET cc_start: 0.8318 (mmt) cc_final: 0.8116 (mmt) REVERT: A 521 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8508 (mt) REVERT: A 577 LYS cc_start: 0.7862 (mmmm) cc_final: 0.7621 (mmtp) REVERT: A 584 GLU cc_start: 0.4962 (OUTLIER) cc_final: 0.4085 (mt-10) outliers start: 14 outliers final: 9 residues processed: 76 average time/residue: 0.0420 time to fit residues: 4.5628 Evaluate side-chains 78 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 584 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 22 optimal weight: 0.0370 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.154071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121860 restraints weight = 5343.930| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.94 r_work: 0.3258 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4477 Z= 0.103 Angle : 0.497 6.246 6109 Z= 0.249 Chirality : 0.037 0.132 674 Planarity : 0.004 0.049 743 Dihedral : 5.187 86.214 596 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.00 % Allowed : 14.35 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.37), residues: 542 helix: 1.90 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -1.13 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 499 TYR 0.010 0.001 TYR A 69 PHE 0.015 0.001 PHE A 191 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 4476) covalent geometry : angle 0.49504 / 0.25 ( 6107) SS BOND : bond 0.00715 / 0.38 ( 1) SS BOND : angle 2.47482 / 1.31 ( 2) hydrogen bonds : bond 0.03279 / 2.17 ( 276) hydrogen bonds : angle 4.28960 / 2.98 ( 819) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.159 Fit side-chains REVERT: A 69 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7747 (t80) REVERT: A 86 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.7780 (t80) REVERT: A 164 HIS cc_start: 0.7784 (m-70) cc_final: 0.7267 (m170) REVERT: A 176 MET cc_start: 0.7458 (mmm) cc_final: 0.7142 (mmm) REVERT: A 236 TRP cc_start: 0.8493 (t60) cc_final: 0.7948 (t60) REVERT: A 249 THR cc_start: 0.7628 (m) cc_final: 0.7393 (t) REVERT: A 320 TYR cc_start: 0.8733 (t80) cc_final: 0.8354 (t80) REVERT: A 358 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7740 (t0) REVERT: A 421 PHE cc_start: 0.7584 (t80) cc_final: 0.7267 (t80) REVERT: A 432 ILE cc_start: 0.7741 (mt) cc_final: 0.7524 (mt) REVERT: A 521 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8521 (mt) REVERT: A 577 LYS cc_start: 0.7868 (mmmm) cc_final: 0.7634 (mmtp) REVERT: A 584 GLU cc_start: 0.4894 (OUTLIER) cc_final: 0.4093 (mt-10) outliers start: 14 outliers final: 9 residues processed: 78 average time/residue: 0.0461 time to fit residues: 5.1581 Evaluate side-chains 78 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 584 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.151161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118570 restraints weight = 5404.594| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.93 r_work: 0.3222 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4477 Z= 0.126 Angle : 0.516 6.572 6109 Z= 0.260 Chirality : 0.038 0.130 674 Planarity : 0.004 0.047 743 Dihedral : 5.251 86.017 596 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.00 % Allowed : 14.13 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.37), residues: 542 helix: 1.81 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -1.08 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 201 TYR 0.014 0.001 TYR A 69 PHE 0.015 0.001 PHE A 95 TRP 0.018 0.001 TRP A 166 HIS 0.005 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 4476) covalent geometry : angle 0.51461 / 0.26 ( 6107) SS BOND : bond 0.00514 / 0.27 ( 1) SS BOND : angle 1.81701 / 0.97 ( 2) hydrogen bonds : bond 0.03590 / 2.37 ( 276) hydrogen bonds : angle 4.34409 / 3.01 ( 819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1154.82 seconds wall clock time: 20 minutes 27.27 seconds (1227.27 seconds total)