Starting phenix.real_space_refine on Wed Sep 17 04:31:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bc6_12140/09_2025/7bc6_12140.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bc6_12140/09_2025/7bc6_12140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bc6_12140/09_2025/7bc6_12140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bc6_12140/09_2025/7bc6_12140.map" model { file = "/net/cci-nas-00/data/ceres_data/7bc6_12140/09_2025/7bc6_12140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bc6_12140/09_2025/7bc6_12140.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2714 2.51 5 N 695 2.21 5 O 747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4178 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3269 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 17, 'TRANS': 414} Chain: "B" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 909 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Time building chain proxies: 1.38, per 1000 atoms: 0.33 Number of scatterers: 4178 At special positions: 0 Unit cell: (106.496, 64.896, 64.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 747 8.00 N 695 7.00 C 2714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 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 178.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 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: 19 helices and 2 sheets defined 64.1% alpha, 4.7% 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 29 through 59 Proline residue: A 45 - end of helix removed outlier: 3.582A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 120 removed outlier: 3.989A pdb=" N THR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.708A pdb=" N SER A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 146 Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 149 through 162 removed outlier: 4.060A pdb=" N LEU A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 178 Processing helix chain 'A' and resid 184 through 207 removed outlier: 3.717A pdb=" N LEU A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.583A pdb=" N LYS A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 220 through 238 removed outlier: 3.529A pdb=" N LEU A 224 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 264 removed outlier: 3.747A pdb=" N TYR A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 301 removed outlier: 3.638A pdb=" N ALA A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 334 removed outlier: 3.566A pdb=" N ILE A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU A 324 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 359 Processing helix chain 'A' and resid 362 through 373 Processing helix chain 'A' and resid 374 through 378 removed outlier: 5.583A pdb=" N MET A 377 " --> pdb=" O PHE A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 395 through 425 removed outlier: 3.549A pdb=" N PHE A 400 " --> pdb=" O GLN A 396 " (cutoff:3.500A) Proline residue: A 423 - end of helix Processing helix chain 'A' and resid 431 through 441 Processing helix chain 'A' and resid 441 through 457 removed outlier: 3.550A pdb=" N ALA A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.611A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 771 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: 0.69 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 651 1.30 - 1.43: 1173 1.43 - 1.56: 2421 1.56 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 4278 Sorted by residual: bond pdb=" CA SER A 349 " pdb=" CB SER A 349 " ideal model delta sigma weight residual 1.528 1.441 0.087 1.56e-02 4.11e+03 3.12e+01 bond pdb=" CA SER A 326 " pdb=" CB SER A 326 " ideal model delta sigma weight residual 1.529 1.441 0.088 1.62e-02 3.81e+03 2.97e+01 bond pdb=" C ASN A 350 " pdb=" O ASN A 350 " ideal model delta sigma weight residual 1.237 1.175 0.062 1.17e-02 7.31e+03 2.81e+01 bond pdb=" CA SER A 325 " pdb=" CB SER A 325 " ideal model delta sigma weight residual 1.528 1.443 0.085 1.66e-02 3.63e+03 2.62e+01 bond pdb=" C ILE A 348 " pdb=" O ILE A 348 " ideal model delta sigma weight residual 1.237 1.177 0.060 1.19e-02 7.06e+03 2.52e+01 ... (remaining 4273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 5452 1.53 - 3.07: 263 3.07 - 4.60: 76 4.60 - 6.13: 26 6.13 - 7.66: 10 Bond angle restraints: 5827 Sorted by residual: angle pdb=" CA TYR A 296 " pdb=" C TYR A 296 " pdb=" O TYR A 296 " ideal model delta sigma weight residual 121.00 113.56 7.44 1.05e+00 9.07e-01 5.02e+01 angle pdb=" N LEU A 321 " pdb=" CA LEU A 321 " pdb=" C LEU A 321 " ideal model delta sigma weight residual 113.72 106.18 7.54 1.30e+00 5.92e-01 3.37e+01 angle pdb=" CA TYR A 296 " pdb=" C TYR A 296 " pdb=" N VAL A 297 " ideal model delta sigma weight residual 116.92 123.28 -6.36 1.16e+00 7.43e-01 3.01e+01 angle pdb=" CA VAL A 297 " pdb=" C VAL A 297 " pdb=" O VAL A 297 " ideal model delta sigma weight residual 120.95 115.55 5.40 1.04e+00 9.25e-01 2.69e+01 angle pdb=" N LEU A 327 " pdb=" CA LEU A 327 " pdb=" C LEU A 327 " ideal model delta sigma weight residual 112.38 106.17 6.21 1.22e+00 6.72e-01 2.59e+01 ... (remaining 5822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 2254 17.69 - 35.37: 195 35.37 - 53.06: 35 53.06 - 70.74: 5 70.74 - 88.43: 2 Dihedral angle restraints: 2491 sinusoidal: 926 harmonic: 1565 Sorted by residual: dihedral pdb=" CA SER B 49 " pdb=" C SER B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" N VAL A 297 " pdb=" C VAL A 297 " pdb=" CA VAL A 297 " pdb=" CB VAL A 297 " ideal model delta harmonic sigma weight residual 123.40 131.76 -8.36 0 2.50e+00 1.60e-01 1.12e+01 dihedral pdb=" CA ASN A 350 " pdb=" CB ASN A 350 " pdb=" CG ASN A 350 " pdb=" OD1 ASN A 350 " ideal model delta sinusoidal sigma weight residual 120.00 -167.54 -72.46 2 2.00e+01 2.50e-03 1.09e+01 ... (remaining 2488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 474 0.045 - 0.091: 147 0.091 - 0.136: 36 0.136 - 0.181: 8 0.181 - 0.227: 6 Chirality restraints: 671 Sorted by residual: chirality pdb=" CA SER A 349 " pdb=" N SER A 349 " pdb=" C SER A 349 " pdb=" CB SER A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA LEU A 324 " pdb=" N LEU A 324 " pdb=" C LEU A 324 " pdb=" CB LEU A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LEU A 327 " pdb=" N LEU A 327 " pdb=" C LEU A 327 " pdb=" CB LEU A 327 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 668 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 320 " 0.044 2.00e-02 2.50e+03 8.49e-02 7.22e+01 pdb=" C TYR A 320 " -0.147 2.00e-02 2.50e+03 pdb=" O TYR A 320 " 0.054 2.00e-02 2.50e+03 pdb=" N LEU A 321 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 349 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C SER A 349 " -0.056 2.00e-02 2.50e+03 pdb=" O SER A 349 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 350 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 295 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C LEU A 295 " 0.055 2.00e-02 2.50e+03 pdb=" O LEU A 295 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR A 296 " -0.019 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 148 2.70 - 3.25: 4141 3.25 - 3.80: 6746 3.80 - 4.35: 8844 4.35 - 4.90: 15282 Nonbonded interactions: 35161 Sorted by model distance: nonbonded pdb=" NH2 ARG A 83 " pdb=" OE2 GLU B 107 " model vdw 2.145 3.120 nonbonded pdb=" NH2 ARG A 122 " pdb=" O LEU A 238 " model vdw 2.160 3.120 nonbonded pdb=" OG SER A 76 " pdb=" OE1 GLN B 39 " model vdw 2.171 3.040 nonbonded pdb=" N ALA A 26 " pdb=" O CYS A 237 " model vdw 2.211 3.120 nonbonded pdb=" OD1 ASP A 53 " pdb=" ND2 ASN A 65 " model vdw 2.214 3.120 ... (remaining 35156 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.820 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.008 0.088 4280 Z= 0.418 Angle : 0.901 7.664 5831 Z= 0.559 Chirality : 0.051 0.227 671 Planarity : 0.006 0.085 728 Dihedral : 13.654 88.430 1493 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.92 % Allowed : 0.92 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.34), residues: 545 helix: -0.07 (0.27), residues: 331 sheet: -3.73 (0.57), residues: 46 loop : -2.49 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 430 TYR 0.026 0.002 TYR A 299 PHE 0.020 0.002 PHE A 220 TRP 0.010 0.001 TRP B 36 HIS 0.008 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00769 ( 4278) covalent geometry : angle 0.90079 ( 5827) SS BOND : bond 0.00439 ( 2) SS BOND : angle 0.56425 ( 4) hydrogen bonds : bond 0.15272 ( 260) hydrogen bonds : angle 6.74593 ( 771) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.126 Fit side-chains REVERT: A 321 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7743 (mt) REVERT: A 348 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7527 (mp) REVERT: B 90 ASP cc_start: 0.7949 (m-30) cc_final: 0.7597 (m-30) outliers start: 4 outliers final: 1 residues processed: 54 average time/residue: 0.0517 time to fit residues: 3.8533 Evaluate side-chains 44 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 350 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.142467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125990 restraints weight = 4592.949| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.84 r_work: 0.3149 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4280 Z= 0.159 Angle : 0.628 7.273 5831 Z= 0.313 Chirality : 0.042 0.175 671 Planarity : 0.005 0.051 728 Dihedral : 6.558 74.536 604 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.83 % Allowed : 6.64 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.36), residues: 545 helix: 0.66 (0.28), residues: 342 sheet: -3.39 (0.61), residues: 46 loop : -2.56 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 430 TYR 0.012 0.001 TYR A 50 PHE 0.014 0.002 PHE A 283 TRP 0.004 0.001 TRP A 93 HIS 0.007 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 4278) covalent geometry : angle 0.62851 ( 5827) SS BOND : bond 0.00516 ( 2) SS BOND : angle 0.34300 ( 4) hydrogen bonds : bond 0.04480 ( 260) hydrogen bonds : angle 4.62303 ( 771) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.171 Fit side-chains REVERT: A 350 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.8025 (t0) REVERT: A 429 MET cc_start: 0.6847 (ttt) cc_final: 0.6561 (ttt) REVERT: B 73 ASP cc_start: 0.7583 (t70) cc_final: 0.6732 (t70) REVERT: B 90 ASP cc_start: 0.8022 (m-30) cc_final: 0.7705 (m-30) outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.0463 time to fit residues: 3.4482 Evaluate side-chains 45 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.0370 chunk 19 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.128404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.112646 restraints weight = 4725.546| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.69 r_work: 0.3194 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4280 Z= 0.132 Angle : 0.580 6.830 5831 Z= 0.287 Chirality : 0.041 0.159 671 Planarity : 0.005 0.048 728 Dihedral : 5.774 62.572 602 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.06 % Allowed : 8.92 % Favored : 89.02 % 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 aren not related in a simple way. whole: -0.36 (0.37), residues: 545 helix: 1.03 (0.28), residues: 349 sheet: -2.98 (0.59), residues: 56 loop : -2.21 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 430 TYR 0.010 0.001 TYR A 50 PHE 0.014 0.001 PHE A 283 TRP 0.005 0.001 TRP B 36 HIS 0.007 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4278) covalent geometry : angle 0.58019 ( 5827) SS BOND : bond 0.00428 ( 2) SS BOND : angle 0.35836 ( 4) hydrogen bonds : bond 0.03960 ( 260) hydrogen bonds : angle 4.25589 ( 771) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.105 Fit side-chains REVERT: A 321 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7104 (mt) REVERT: A 429 MET cc_start: 0.6874 (ttt) cc_final: 0.6455 (ttt) REVERT: B 90 ASP cc_start: 0.7982 (m-30) cc_final: 0.7674 (m-30) outliers start: 9 outliers final: 5 residues processed: 47 average time/residue: 0.0358 time to fit residues: 2.5420 Evaluate side-chains 39 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.0670 chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.128058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.111366 restraints weight = 4699.652| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.83 r_work: 0.3197 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4280 Z= 0.155 Angle : 0.600 6.643 5831 Z= 0.297 Chirality : 0.041 0.152 671 Planarity : 0.005 0.048 728 Dihedral : 4.962 46.316 600 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.20 % Allowed : 9.61 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.37), residues: 545 helix: 1.10 (0.28), residues: 349 sheet: -2.75 (0.60), residues: 56 loop : -2.19 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 59 TYR 0.012 0.001 TYR A 50 PHE 0.012 0.002 PHE A 283 TRP 0.005 0.001 TRP B 36 HIS 0.007 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 4278) covalent geometry : angle 0.60031 ( 5827) SS BOND : bond 0.00377 ( 2) SS BOND : angle 0.33637 ( 4) hydrogen bonds : bond 0.04132 ( 260) hydrogen bonds : angle 4.29587 ( 771) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.161 Fit side-chains REVERT: A 321 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7060 (mt) REVERT: A 429 MET cc_start: 0.6956 (ttt) cc_final: 0.6560 (ttt) REVERT: B 90 ASP cc_start: 0.8041 (m-30) cc_final: 0.7738 (m-30) outliers start: 14 outliers final: 9 residues processed: 50 average time/residue: 0.0427 time to fit residues: 3.1897 Evaluate side-chains 44 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.143514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.126751 restraints weight = 4527.810| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.88 r_work: 0.3185 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4280 Z= 0.123 Angle : 0.570 6.776 5831 Z= 0.283 Chirality : 0.040 0.150 671 Planarity : 0.004 0.047 728 Dihedral : 4.495 41.259 600 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.06 % Allowed : 11.67 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.37), residues: 545 helix: 1.38 (0.28), residues: 347 sheet: -2.53 (0.59), residues: 58 loop : -2.07 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 430 TYR 0.009 0.001 TYR A 50 PHE 0.014 0.001 PHE A 283 TRP 0.004 0.001 TRP B 36 HIS 0.007 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4278) covalent geometry : angle 0.57052 ( 5827) SS BOND : bond 0.00338 ( 2) SS BOND : angle 0.30215 ( 4) hydrogen bonds : bond 0.03728 ( 260) hydrogen bonds : angle 4.07266 ( 771) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.128 Fit side-chains REVERT: A 321 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7558 (mt) REVERT: B 90 ASP cc_start: 0.7972 (m-30) cc_final: 0.7699 (m-30) outliers start: 9 outliers final: 7 residues processed: 46 average time/residue: 0.0425 time to fit residues: 2.8407 Evaluate side-chains 44 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 41 optimal weight: 0.0040 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.134737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117009 restraints weight = 4727.046| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.00 r_work: 0.3098 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4280 Z= 0.139 Angle : 0.590 7.182 5831 Z= 0.291 Chirality : 0.041 0.161 671 Planarity : 0.004 0.046 728 Dihedral : 4.526 47.888 600 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.97 % Allowed : 12.13 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.37), residues: 545 helix: 1.35 (0.28), residues: 349 sheet: -2.28 (0.62), residues: 58 loop : -2.15 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 59 TYR 0.012 0.001 TYR A 50 PHE 0.013 0.002 PHE A 283 TRP 0.004 0.001 TRP B 36 HIS 0.007 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4278) covalent geometry : angle 0.59030 ( 5827) SS BOND : bond 0.00332 ( 2) SS BOND : angle 0.32541 ( 4) hydrogen bonds : bond 0.03917 ( 260) hydrogen bonds : angle 4.13900 ( 771) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.155 Fit side-chains REVERT: A 321 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7329 (mt) REVERT: A 377 MET cc_start: 0.8729 (mmm) cc_final: 0.8165 (mmt) REVERT: B 90 ASP cc_start: 0.8036 (m-30) cc_final: 0.7759 (m-30) outliers start: 13 outliers final: 10 residues processed: 50 average time/residue: 0.0448 time to fit residues: 3.3658 Evaluate side-chains 46 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.133409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116240 restraints weight = 4740.197| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.90 r_work: 0.3119 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4280 Z= 0.135 Angle : 0.584 7.530 5831 Z= 0.288 Chirality : 0.041 0.163 671 Planarity : 0.004 0.047 728 Dihedral : 4.464 47.624 600 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.52 % Allowed : 13.27 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.37), residues: 545 helix: 1.46 (0.28), residues: 346 sheet: -2.18 (0.63), residues: 58 loop : -2.03 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 59 TYR 0.010 0.001 TYR A 50 PHE 0.013 0.001 PHE A 283 TRP 0.005 0.001 TRP B 36 HIS 0.007 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4278) covalent geometry : angle 0.58448 ( 5827) SS BOND : bond 0.00321 ( 2) SS BOND : angle 0.30685 ( 4) hydrogen bonds : bond 0.03871 ( 260) hydrogen bonds : angle 4.11722 ( 771) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.159 Fit side-chains REVERT: A 377 MET cc_start: 0.8700 (mmm) cc_final: 0.8141 (mmt) REVERT: B 90 ASP cc_start: 0.7991 (m-30) cc_final: 0.7705 (m-30) outliers start: 11 outliers final: 9 residues processed: 48 average time/residue: 0.0446 time to fit residues: 3.1810 Evaluate side-chains 44 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.142539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.126016 restraints weight = 4578.400| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.85 r_work: 0.3172 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4280 Z= 0.155 Angle : 0.604 7.377 5831 Z= 0.298 Chirality : 0.041 0.165 671 Planarity : 0.004 0.047 728 Dihedral : 4.107 15.935 598 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.20 % Allowed : 12.59 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.37), residues: 545 helix: 1.38 (0.28), residues: 347 sheet: -2.21 (0.63), residues: 58 loop : -2.09 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 59 TYR 0.013 0.001 TYR A 50 PHE 0.012 0.002 PHE A 283 TRP 0.004 0.001 TRP B 36 HIS 0.008 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 4278) covalent geometry : angle 0.60453 ( 5827) SS BOND : bond 0.00352 ( 2) SS BOND : angle 0.30481 ( 4) hydrogen bonds : bond 0.04070 ( 260) hydrogen bonds : angle 4.19182 ( 771) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.168 Fit side-chains REVERT: A 377 MET cc_start: 0.8759 (mmm) cc_final: 0.8194 (mmt) REVERT: B 90 ASP cc_start: 0.8023 (m-30) cc_final: 0.7743 (m-30) outliers start: 14 outliers final: 11 residues processed: 54 average time/residue: 0.0391 time to fit residues: 3.2527 Evaluate side-chains 48 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.143134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126482 restraints weight = 4608.993| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.85 r_work: 0.3153 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4280 Z= 0.150 Angle : 0.608 7.552 5831 Z= 0.300 Chirality : 0.041 0.164 671 Planarity : 0.004 0.046 728 Dihedral : 4.100 16.326 598 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.52 % Allowed : 14.87 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.37), residues: 545 helix: 1.38 (0.28), residues: 347 sheet: -2.18 (0.63), residues: 58 loop : -2.03 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 59 TYR 0.032 0.002 TYR B 60 PHE 0.013 0.002 PHE A 283 TRP 0.004 0.001 TRP B 36 HIS 0.009 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4278) covalent geometry : angle 0.60821 ( 5827) SS BOND : bond 0.00335 ( 2) SS BOND : angle 0.27079 ( 4) hydrogen bonds : bond 0.04019 ( 260) hydrogen bonds : angle 4.17555 ( 771) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.165 Fit side-chains REVERT: A 377 MET cc_start: 0.8732 (mmm) cc_final: 0.8132 (mmt) REVERT: B 90 ASP cc_start: 0.7983 (m-30) cc_final: 0.7688 (m-30) outliers start: 11 outliers final: 10 residues processed: 47 average time/residue: 0.0460 time to fit residues: 3.2603 Evaluate side-chains 45 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.0020 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.146943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.130193 restraints weight = 4478.436| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.90 r_work: 0.3201 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4280 Z= 0.119 Angle : 0.575 7.672 5831 Z= 0.283 Chirality : 0.040 0.164 671 Planarity : 0.004 0.046 728 Dihedral : 3.891 16.758 598 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.52 % Allowed : 14.87 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.37), residues: 545 helix: 1.57 (0.28), residues: 347 sheet: -1.92 (0.67), residues: 58 loop : -1.83 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 430 TYR 0.017 0.001 TYR B 60 PHE 0.014 0.001 PHE A 283 TRP 0.005 0.001 TRP B 36 HIS 0.007 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4278) covalent geometry : angle 0.57475 ( 5827) SS BOND : bond 0.00289 ( 2) SS BOND : angle 0.23045 ( 4) hydrogen bonds : bond 0.03630 ( 260) hydrogen bonds : angle 3.98399 ( 771) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.163 Fit side-chains REVERT: A 377 MET cc_start: 0.8725 (mmm) cc_final: 0.8183 (mmt) REVERT: B 90 ASP cc_start: 0.7959 (m-30) cc_final: 0.7681 (m-30) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 0.0499 time to fit residues: 3.4502 Evaluate side-chains 44 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.0170 chunk 12 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 36 optimal weight: 0.0030 chunk 43 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.0570 chunk 14 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 overall best weight: 0.2546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.151367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134483 restraints weight = 4516.135| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.92 r_work: 0.3250 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4280 Z= 0.109 Angle : 0.563 9.839 5831 Z= 0.278 Chirality : 0.040 0.166 671 Planarity : 0.004 0.047 728 Dihedral : 3.706 16.595 598 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.83 % Allowed : 16.25 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.37), residues: 545 helix: 1.76 (0.28), residues: 347 sheet: -2.21 (0.61), residues: 64 loop : -1.65 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 430 TYR 0.014 0.001 TYR B 60 PHE 0.015 0.001 PHE A 283 TRP 0.007 0.001 TRP A 52 HIS 0.008 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 4278) covalent geometry : angle 0.56332 ( 5827) SS BOND : bond 0.00255 ( 2) SS BOND : angle 0.20061 ( 4) hydrogen bonds : bond 0.03388 ( 260) hydrogen bonds : angle 3.82594 ( 771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1266.49 seconds wall clock time: 22 minutes 29.34 seconds (1349.34 seconds total)