Starting phenix.real_space_refine on Thu Jul 2 00:18:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmp_66100/07_2026/9wmp_66100_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmp_66100/07_2026/9wmp_66100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wmp_66100/07_2026/9wmp_66100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmp_66100/07_2026/9wmp_66100.map" model { file = "/net/cci-nas-00/data/ceres_data/9wmp_66100/07_2026/9wmp_66100_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmp_66100/07_2026/9wmp_66100_neut.cif" } resolution = 2.91 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= -0.003 sd= 0.103 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 3019 2.51 5 N 657 2.21 5 O 721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 4433 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4263 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 26, 'TRANS': 513} Chain breaks: 1 Chain: "A" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 168 Ad-hoc single atom residues: {' NA': 1, ' CL': 1} Unusual residues: {'CLR': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 2 Time building chain proxies: 1.27, per 1000 atoms: 0.29 Number of scatterers: 4433 At special positions: 0 Unit cell: (82.159, 69.355, 82.159, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 1 11.00 O 721 8.00 N 657 7.00 C 3019 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 166 " 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: 0.40 Conformation dependent library (CDL) restraints added in 207.0 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 982 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 78.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.537A pdb=" N LEU A 44 " --> pdb=" O TRP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 72 through 86 Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 86 through 102 removed outlier: 3.548A pdb=" N LEU A 90 " --> pdb=" O CYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.601A pdb=" N TRP A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 115 through 147 removed outlier: 3.994A pdb=" N GLY A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 4.190A pdb=" N HIS A 156 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 214 through 234 Processing helix chain 'A' and resid 247 through 264 removed outlier: 3.517A pdb=" N THR A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 removed outlier: 4.042A pdb=" N GLY A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 284 through 300 removed outlier: 4.243A pdb=" N TRP A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.823A pdb=" N TYR A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 353 Processing helix chain 'A' and resid 365 through 376 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 380 through 415 removed outlier: 3.563A pdb=" N TRP A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 439 Processing helix chain 'A' and resid 440 through 443 removed outlier: 3.791A pdb=" N THR A 443 " --> pdb=" O ILE A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.643A pdb=" N TRP A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 532 through 561 removed outlier: 3.839A pdb=" N SER A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Proline residue: A 551 - end of helix Processing helix chain 'A' and resid 564 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 525 through 526 290 hydrogen bonds defined for protein. 846 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: 0.72 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 626 1.31 - 1.44: 1320 1.44 - 1.56: 2580 1.56 - 1.69: 2 1.69 - 1.81: 54 Bond restraints: 4582 Sorted by residual: bond pdb=" C SER A 381 " pdb=" O SER A 381 " ideal model delta sigma weight residual 1.238 1.186 0.051 1.28e-02 6.10e+03 1.62e+01 bond pdb=" N SER A 381 " pdb=" CA SER A 381 " ideal model delta sigma weight residual 1.457 1.506 -0.049 1.41e-02 5.03e+03 1.21e+01 bond pdb=" N ILE A 325 " pdb=" CA ILE A 325 " ideal model delta sigma weight residual 1.461 1.500 -0.040 1.19e-02 7.06e+03 1.11e+01 bond pdb=" C ILE A 479 " pdb=" O ILE A 479 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.32e-02 5.74e+03 1.08e+01 bond pdb=" N GLN A 522 " pdb=" CA GLN A 522 " ideal model delta sigma weight residual 1.462 1.496 -0.033 1.05e-02 9.07e+03 1.01e+01 ... (remaining 4577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 6004 2.14 - 4.28: 240 4.28 - 6.42: 32 6.42 - 8.56: 4 8.56 - 10.70: 1 Bond angle restraints: 6281 Sorted by residual: angle pdb=" N ARG A 321 " pdb=" CA ARG A 321 " pdb=" C ARG A 321 " ideal model delta sigma weight residual 111.11 105.37 5.74 1.20e+00 6.94e-01 2.29e+01 angle pdb=" CA LEU A 395 " pdb=" C LEU A 395 " pdb=" O LEU A 395 " ideal model delta sigma weight residual 120.82 116.33 4.49 1.05e+00 9.07e-01 1.83e+01 angle pdb=" CA SER A 298 " pdb=" C SER A 298 " pdb=" O SER A 298 " ideal model delta sigma weight residual 120.82 116.64 4.18 1.05e+00 9.07e-01 1.58e+01 angle pdb=" CA LEU A 503 " pdb=" C LEU A 503 " pdb=" O LEU A 503 " ideal model delta sigma weight residual 120.42 116.31 4.11 1.06e+00 8.90e-01 1.50e+01 angle pdb=" N MET A 135 " pdb=" CA MET A 135 " pdb=" C MET A 135 " ideal model delta sigma weight residual 111.71 107.30 4.41 1.15e+00 7.56e-01 1.47e+01 ... (remaining 6276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 2627 23.98 - 47.95: 209 47.95 - 71.92: 36 71.92 - 95.90: 1 95.90 - 119.87: 13 Dihedral angle restraints: 2886 sinusoidal: 1336 harmonic: 1550 Sorted by residual: dihedral pdb=" C1 CLR A 707 " pdb=" C2 CLR A 707 " pdb=" C3 CLR A 707 " pdb=" O1 CLR A 707 " ideal model delta sinusoidal sigma weight residual 180.04 60.17 119.87 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C10 CLR A 706 " pdb=" C1 CLR A 706 " pdb=" C2 CLR A 706 " pdb=" C3 CLR A 706 " ideal model delta sinusoidal sigma weight residual -56.83 62.25 -119.08 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" C1 CLR A 707 " pdb=" C2 CLR A 707 " pdb=" C3 CLR A 707 " pdb=" C4 CLR A 707 " ideal model delta sinusoidal sigma weight residual 57.41 -61.45 118.86 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 2883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 534 0.044 - 0.089: 114 0.089 - 0.133: 57 0.133 - 0.177: 14 0.177 - 0.221: 3 Chirality restraints: 722 Sorted by residual: chirality pdb=" CA ASN A 134 " pdb=" N ASN A 134 " pdb=" C ASN A 134 " pdb=" CB ASN A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA GLN A 400 " pdb=" N GLN A 400 " pdb=" C GLN A 400 " pdb=" CB GLN A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA MET A 122 " pdb=" N MET A 122 " pdb=" C MET A 122 " pdb=" CB MET A 122 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.06e-01 ... (remaining 719 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 321 " -0.019 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C ARG A 321 " 0.064 2.00e-02 2.50e+03 pdb=" O ARG A 321 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP A 322 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 402 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C ALA A 402 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA A 402 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE A 403 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 522 " 0.044 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO A 523 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 523 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 523 " 0.036 5.00e-02 4.00e+02 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1556 2.86 - 3.37: 4465 3.37 - 3.88: 7916 3.88 - 4.39: 9598 4.39 - 4.90: 15541 Nonbonded interactions: 39076 Sorted by model distance: nonbonded pdb=" O LEU A 144 " pdb=" OG SER A 147 " model vdw 2.345 3.040 nonbonded pdb=" OG SER A 298 " pdb="NA NA A 701 " model vdw 2.354 3.210 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 536 " model vdw 2.383 3.040 nonbonded pdb=" OD1 ASN A 59 " pdb="NA NA A 701 " model vdw 2.424 3.210 nonbonded pdb=" O PHE A 339 " pdb=" OG SER A 343 " model vdw 2.433 3.040 ... (remaining 39071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.790 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.005 0.058 4583 Z= 0.356 Angle : 0.891 10.699 6283 Z= 0.560 Chirality : 0.049 0.221 722 Planarity : 0.007 0.066 726 Dihedral : 18.705 119.873 1901 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 18.98 % Favored : 81.02 % 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: 0.24 (0.35), residues: 536 helix: 0.86 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.43 (0.44), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 420 TYR 0.016 0.002 TYR A 132 PHE 0.012 0.001 PHE A 245 TRP 0.027 0.002 TRP A 215 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.36 ( 4582) covalent geometry : angle 0.89127 / 0.56 ( 6281) SS BOND : bond 0.00293 / 0.15 ( 1) SS BOND : angle 0.51859 / 0.30 ( 2) hydrogen bonds : bond 0.12732 / 8.32 ( 290) hydrogen bonds : angle 6.03806 / 4.13 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.155 Fit side-chains REVERT: A 312 TYR cc_start: 0.8058 (m-80) cc_final: 0.7745 (m-80) REVERT: A 358 GLN cc_start: 0.7820 (pt0) cc_final: 0.7548 (pp30) REVERT: A 414 GLU cc_start: 0.7565 (tp30) cc_final: 0.7355 (tp30) outliers start: 0 outliers final: 1 residues processed: 91 average time/residue: 0.5243 time to fit residues: 49.4628 Evaluate side-chains 57 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.0270 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.122325 restraints weight = 5334.515| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.50 r_work: 0.3196 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4583 Z= 0.140 Angle : 0.598 6.334 6283 Z= 0.285 Chirality : 0.038 0.154 722 Planarity : 0.005 0.056 726 Dihedral : 9.218 57.265 976 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.09 % Allowed : 17.88 % Favored : 79.03 % 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: 1.51 (0.36), residues: 536 helix: 1.84 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -1.05 (0.46), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 530 TYR 0.017 0.001 TYR A 132 PHE 0.014 0.001 PHE A 245 TRP 0.015 0.001 TRP A 215 HIS 0.001 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 4582) covalent geometry : angle 0.59818 / 0.28 ( 6281) SS BOND : bond 0.00232 / 0.12 ( 1) SS BOND : angle 0.19941 / 0.11 ( 2) hydrogen bonds : bond 0.04356 / 2.82 ( 290) hydrogen bonds : angle 4.66800 / 3.22 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7838 (tp30) REVERT: A 312 TYR cc_start: 0.8337 (m-80) cc_final: 0.7845 (m-80) REVERT: A 357 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7642 (p0) REVERT: A 358 GLN cc_start: 0.8174 (pt0) cc_final: 0.7551 (pm20) REVERT: A 414 GLU cc_start: 0.7628 (tp30) cc_final: 0.7366 (tp30) REVERT: A 525 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7747 (mt-10) REVERT: A 571 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7852 (mp10) outliers start: 14 outliers final: 3 residues processed: 71 average time/residue: 0.4437 time to fit residues: 33.0656 Evaluate side-chains 64 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 571 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 0.0470 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.144413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127520 restraints weight = 5327.513| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.44 r_work: 0.3203 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4583 Z= 0.110 Angle : 0.504 5.348 6283 Z= 0.245 Chirality : 0.037 0.155 722 Planarity : 0.004 0.047 726 Dihedral : 8.420 57.727 974 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.65 % Allowed : 19.21 % Favored : 78.15 % 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: 1.97 (0.36), residues: 536 helix: 2.21 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.94 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 568 TYR 0.016 0.001 TYR A 132 PHE 0.010 0.001 PHE A 91 TRP 0.010 0.001 TRP A 215 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 4582) covalent geometry : angle 0.50408 / 0.25 ( 6281) SS BOND : bond 0.00116 / 0.06 ( 1) SS BOND : angle 0.16732 / 0.09 ( 2) hydrogen bonds : bond 0.04070 / 2.62 ( 290) hydrogen bonds : angle 4.43237 / 3.06 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.8315 (tpt) cc_final: 0.7693 (tpt) REVERT: A 187 VAL cc_start: 0.8268 (t) cc_final: 0.7849 (p) REVERT: A 191 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: A 312 TYR cc_start: 0.8491 (m-80) cc_final: 0.8176 (m-80) REVERT: A 358 GLN cc_start: 0.8305 (pt0) cc_final: 0.7705 (pm20) REVERT: A 525 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7619 (mt-10) outliers start: 12 outliers final: 4 residues processed: 74 average time/residue: 0.4739 time to fit residues: 36.6820 Evaluate side-chains 66 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 542 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 0.6980 chunk 51 optimal weight: 0.0070 chunk 53 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN A 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.145180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128851 restraints weight = 5226.256| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.37 r_work: 0.3214 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4583 Z= 0.126 Angle : 0.511 5.408 6283 Z= 0.248 Chirality : 0.038 0.147 722 Planarity : 0.004 0.040 726 Dihedral : 8.293 59.844 974 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.43 % Allowed : 19.43 % Favored : 78.15 % 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: 2.09 (0.36), residues: 536 helix: 2.30 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.87 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 568 TYR 0.012 0.001 TYR A 132 PHE 0.009 0.001 PHE A 389 TRP 0.008 0.001 TRP A 225 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 4582) covalent geometry : angle 0.51146 / 0.25 ( 6281) SS BOND : bond 0.00087 / 0.05 ( 1) SS BOND : angle 0.22271 / 0.12 ( 2) hydrogen bonds : bond 0.04069 / 2.63 ( 290) hydrogen bonds : angle 4.38520 / 3.03 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8167 (mp) cc_final: 0.7912 (tt) REVERT: A 191 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8194 (tp30) REVERT: A 312 TYR cc_start: 0.8492 (m-80) cc_final: 0.8278 (m-80) REVERT: A 348 MET cc_start: 0.8625 (mtp) cc_final: 0.8290 (mtp) REVERT: A 358 GLN cc_start: 0.8308 (pt0) cc_final: 0.8004 (pt0) REVERT: A 525 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7772 (mt-10) REVERT: A 555 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7617 (tp) REVERT: A 571 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8151 (mp10) outliers start: 11 outliers final: 5 residues processed: 68 average time/residue: 0.4581 time to fit residues: 32.7095 Evaluate side-chains 68 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 571 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.134520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116141 restraints weight = 5394.757| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.52 r_work: 0.3205 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4583 Z= 0.139 Angle : 0.519 5.332 6283 Z= 0.250 Chirality : 0.038 0.157 722 Planarity : 0.004 0.036 726 Dihedral : 8.130 58.035 974 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.43 % Allowed : 19.21 % Favored : 78.37 % 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: 2.13 (0.36), residues: 536 helix: 2.31 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.83 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.015 0.001 TYR A 132 PHE 0.011 0.001 PHE A 303 TRP 0.008 0.001 TRP A 225 HIS 0.003 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 4582) covalent geometry : angle 0.51867 / 0.25 ( 6281) SS BOND : bond 0.00075 / 0.04 ( 1) SS BOND : angle 0.16940 / 0.09 ( 2) hydrogen bonds : bond 0.04152 / 2.67 ( 290) hydrogen bonds : angle 4.39553 / 3.04 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 85 ILE cc_start: 0.7980 (mp) cc_final: 0.7637 (tt) REVERT: A 312 TYR cc_start: 0.8643 (m-80) cc_final: 0.8284 (m-80) REVERT: A 358 GLN cc_start: 0.8245 (pt0) cc_final: 0.8000 (pt0) REVERT: A 516 TYR cc_start: 0.8179 (m-80) cc_final: 0.7875 (m-80) REVERT: A 525 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7701 (mt-10) REVERT: A 555 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7446 (tp) REVERT: A 571 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7827 (mp10) outliers start: 11 outliers final: 6 residues processed: 71 average time/residue: 0.4333 time to fit residues: 32.2336 Evaluate side-chains 71 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 571 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.0770 chunk 1 optimal weight: 0.5980 chunk 53 optimal weight: 0.4980 chunk 42 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.127098 restraints weight = 5415.837| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.41 r_work: 0.3198 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4583 Z= 0.120 Angle : 0.501 5.297 6283 Z= 0.243 Chirality : 0.038 0.160 722 Planarity : 0.004 0.033 726 Dihedral : 8.087 58.978 974 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.43 % Allowed : 20.97 % Favored : 76.60 % 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: 2.20 (0.36), residues: 536 helix: 2.39 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -0.85 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.014 0.001 TYR A 132 PHE 0.009 0.001 PHE A 91 TRP 0.008 0.001 TRP A 225 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 4582) covalent geometry : angle 0.50137 / 0.24 ( 6281) SS BOND : bond 0.00038 / 0.02 ( 1) SS BOND : angle 0.19565 / 0.11 ( 2) hydrogen bonds : bond 0.03982 / 2.55 ( 290) hydrogen bonds : angle 4.34476 / 3.01 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8161 (mp) cc_final: 0.7735 (tt) REVERT: A 191 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8029 (tp30) REVERT: A 312 TYR cc_start: 0.8617 (m-80) cc_final: 0.8303 (m-80) REVERT: A 358 GLN cc_start: 0.8316 (pt0) cc_final: 0.8048 (pt0) REVERT: A 516 TYR cc_start: 0.8256 (m-80) cc_final: 0.7936 (m-80) REVERT: A 525 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7687 (mt-10) REVERT: A 555 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7573 (tp) outliers start: 11 outliers final: 6 residues processed: 72 average time/residue: 0.4290 time to fit residues: 32.4724 Evaluate side-chains 71 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 555 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 0.0060 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.146753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130099 restraints weight = 5400.552| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.48 r_work: 0.3155 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4583 Z= 0.132 Angle : 0.512 5.292 6283 Z= 0.249 Chirality : 0.038 0.165 722 Planarity : 0.004 0.032 726 Dihedral : 7.991 59.731 974 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.31 % Allowed : 20.75 % Favored : 75.94 % 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: 2.20 (0.36), residues: 536 helix: 2.36 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.77 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 568 TYR 0.016 0.001 TYR A 132 PHE 0.010 0.001 PHE A 303 TRP 0.008 0.001 TRP A 225 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 4582) covalent geometry : angle 0.51235 / 0.25 ( 6281) SS BOND : bond 0.00044 / 0.02 ( 1) SS BOND : angle 0.22671 / 0.13 ( 2) hydrogen bonds : bond 0.04049 / 2.59 ( 290) hydrogen bonds : angle 4.35829 / 3.02 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8088 (mp) cc_final: 0.7691 (tt) REVERT: A 191 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8032 (tp30) REVERT: A 312 TYR cc_start: 0.8658 (m-80) cc_final: 0.8340 (m-80) REVERT: A 358 GLN cc_start: 0.8293 (pt0) cc_final: 0.8019 (pt0) REVERT: A 516 TYR cc_start: 0.8307 (m-80) cc_final: 0.7957 (m-80) REVERT: A 525 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7685 (mt-10) REVERT: A 549 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8210 (ttt) outliers start: 15 outliers final: 7 residues processed: 74 average time/residue: 0.4144 time to fit residues: 32.1171 Evaluate side-chains 73 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 549 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 49 optimal weight: 0.0060 chunk 34 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131525 restraints weight = 5332.236| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.48 r_work: 0.3174 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4583 Z= 0.118 Angle : 0.507 5.229 6283 Z= 0.246 Chirality : 0.038 0.148 722 Planarity : 0.004 0.032 726 Dihedral : 7.828 59.680 974 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.99 % Allowed : 21.85 % Favored : 76.16 % 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: 2.23 (0.36), residues: 536 helix: 2.37 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.74 (0.49), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 420 TYR 0.016 0.001 TYR A 132 PHE 0.009 0.001 PHE A 91 TRP 0.008 0.001 TRP A 225 HIS 0.001 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 4582) covalent geometry : angle 0.50728 / 0.25 ( 6281) SS BOND : bond 0.00005 / 0.00 ( 1) SS BOND : angle 0.16235 / 0.09 ( 2) hydrogen bonds : bond 0.03925 / 2.53 ( 290) hydrogen bonds : angle 4.29441 / 2.97 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8037 (mp) cc_final: 0.7684 (tt) REVERT: A 191 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8051 (tp30) REVERT: A 312 TYR cc_start: 0.8634 (m-80) cc_final: 0.8325 (m-80) REVERT: A 358 GLN cc_start: 0.8256 (pt0) cc_final: 0.8035 (pt0) REVERT: A 516 TYR cc_start: 0.8310 (m-80) cc_final: 0.7932 (m-80) REVERT: A 549 MET cc_start: 0.8499 (ttm) cc_final: 0.8247 (ttt) outliers start: 9 outliers final: 6 residues processed: 75 average time/residue: 0.4403 time to fit residues: 34.6450 Evaluate side-chains 72 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 546 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.146673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129959 restraints weight = 5387.750| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.49 r_work: 0.3152 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4583 Z= 0.133 Angle : 0.517 5.476 6283 Z= 0.250 Chirality : 0.038 0.153 722 Planarity : 0.004 0.032 726 Dihedral : 7.864 57.367 974 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.65 % Allowed : 22.30 % Favored : 75.06 % 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: 2.14 (0.37), residues: 536 helix: 2.31 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.78 (0.49), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 420 TYR 0.016 0.001 TYR A 132 PHE 0.009 0.001 PHE A 303 TRP 0.008 0.001 TRP A 225 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 4582) covalent geometry : angle 0.51692 / 0.25 ( 6281) SS BOND : bond 0.00175 / 0.09 ( 1) SS BOND : angle 0.48769 / 0.28 ( 2) hydrogen bonds : bond 0.04052 / 2.60 ( 290) hydrogen bonds : angle 4.36592 / 3.02 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8057 (tp30) REVERT: A 205 GLN cc_start: 0.8130 (mp-120) cc_final: 0.7921 (mm-40) REVERT: A 312 TYR cc_start: 0.8655 (m-80) cc_final: 0.8368 (m-80) REVERT: A 358 GLN cc_start: 0.8231 (pt0) cc_final: 0.8020 (pt0) REVERT: A 516 TYR cc_start: 0.8291 (m-80) cc_final: 0.7918 (m-80) REVERT: A 549 MET cc_start: 0.8526 (ttm) cc_final: 0.8277 (ttt) REVERT: A 555 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7479 (tp) outliers start: 12 outliers final: 6 residues processed: 71 average time/residue: 0.3672 time to fit residues: 27.3603 Evaluate side-chains 70 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130978 restraints weight = 5337.366| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.48 r_work: 0.3172 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4583 Z= 0.123 Angle : 0.519 5.963 6283 Z= 0.250 Chirality : 0.038 0.147 722 Planarity : 0.004 0.032 726 Dihedral : 7.779 57.964 974 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.99 % Allowed : 23.18 % Favored : 74.83 % 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: 2.10 (0.37), residues: 536 helix: 2.28 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.80 (0.49), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 420 TYR 0.016 0.001 TYR A 132 PHE 0.008 0.001 PHE A 460 TRP 0.007 0.001 TRP A 225 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 4582) covalent geometry : angle 0.51953 / 0.25 ( 6281) SS BOND : bond 0.00099 / 0.05 ( 1) SS BOND : angle 0.38157 / 0.21 ( 2) hydrogen bonds : bond 0.03976 / 2.56 ( 290) hydrogen bonds : angle 4.33255 / 3.00 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 85 ILE cc_start: 0.7989 (mp) cc_final: 0.7637 (tt) REVERT: A 191 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.7994 (tp30) REVERT: A 205 GLN cc_start: 0.8136 (mp-120) cc_final: 0.7927 (mm-40) REVERT: A 312 TYR cc_start: 0.8652 (m-80) cc_final: 0.8376 (m-80) REVERT: A 516 TYR cc_start: 0.8263 (m-80) cc_final: 0.7907 (m-80) REVERT: A 549 MET cc_start: 0.8508 (ttm) cc_final: 0.8272 (ttt) REVERT: A 555 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7455 (tp) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.4779 time to fit residues: 35.5522 Evaluate side-chains 73 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 0.0030 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 17 optimal weight: 0.0370 chunk 27 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 overall best weight: 0.3268 ------------------------------------------------------------------------------- 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 = 0.149420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.132818 restraints weight = 5394.370| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.50 r_work: 0.3187 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4583 Z= 0.110 Angle : 0.524 10.606 6283 Z= 0.248 Chirality : 0.038 0.176 722 Planarity : 0.004 0.032 726 Dihedral : 7.657 59.480 974 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.21 % Allowed : 22.96 % Favored : 74.83 % 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: 2.16 (0.37), residues: 536 helix: 2.34 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -0.79 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 420 TYR 0.014 0.001 TYR A 132 PHE 0.010 0.001 PHE A 91 TRP 0.007 0.001 TRP A 40 HIS 0.001 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 4582) covalent geometry : angle 0.52404 / 0.25 ( 6281) SS BOND : bond 0.00109 / 0.06 ( 1) SS BOND : angle 0.37830 / 0.21 ( 2) hydrogen bonds : bond 0.03843 / 2.48 ( 290) hydrogen bonds : angle 4.33854 / 3.00 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1631.44 seconds wall clock time: 28 minutes 35.94 seconds (1715.94 seconds total)