Starting phenix.real_space_refine on Thu Jul 2 12:46:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3v_35157/07_2026/8i3v_35157_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3v_35157/07_2026/8i3v_35157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i3v_35157/07_2026/8i3v_35157_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3v_35157/07_2026/8i3v_35157_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i3v_35157/07_2026/8i3v_35157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3v_35157/07_2026/8i3v_35157.map" } resolution = 2.85 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= 0.135 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: 7 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 C 2965 2.51 5 N 681 2.21 5 O 751 1.98 5 F 1 1.80 5 H 4373 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 8792 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8756 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 528} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 35 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'68P': 1} Classifications: {'undetermined': 1, 'water': 11} Link IDs: {None: 10} Chain breaks: 1 Time building chain proxies: 1.47, per 1000 atoms: 0.17 Number of scatterers: 8792 At special positions: 0 Unit cell: (70.3625, 70.3625, 98.5075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 20 16.00 F 1 9.00 O 751 8.00 N 681 7.00 C 2965 6.00 H 4373 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " 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: 0.87 Conformation dependent library (CDL) restraints added in 374.4 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1008 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 1 sheets defined 81.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 60 through 73 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.569A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.560A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.610A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 262 through 283 removed outlier: 3.986A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 3.862A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.575A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.727A pdb=" N GLU A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.734A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.576A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.604A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 496 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.610A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 592 Processing helix chain 'A' and resid 594 through 601 removed outlier: 3.812A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N HIS A 599 " --> pdb=" O ASN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 616 removed outlier: 3.808A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 295 hydrogen bonds defined for protein. 849 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: 1.85 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4366 1.03 - 1.23: 13 1.23 - 1.42: 2017 1.42 - 1.62: 2497 1.62 - 1.81: 31 Bond restraints: 8924 Sorted by residual: bond pdb=" N GLY A 60 " pdb=" CA GLY A 60 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.20e+00 bond pdb=" N GLY A 60 " pdb=" H GLY A 60 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" CA LEU A 102 " pdb=" C LEU A 102 " ideal model delta sigma weight residual 1.524 1.509 0.016 1.28e-02 6.10e+03 1.48e+00 bond pdb=" C23 68P A 701 " pdb=" N03 68P A 701 " ideal model delta sigma weight residual 1.447 1.467 -0.020 2.00e-02 2.50e+03 9.68e-01 bond pdb=" C05 68P A 701 " pdb=" O02 68P A 701 " ideal model delta sigma weight residual 1.420 1.440 -0.020 2.00e-02 2.50e+03 9.59e-01 ... (remaining 8919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.28: 16077 7.28 - 14.56: 0 14.56 - 21.84: 0 21.84 - 29.12: 0 29.12 - 36.40: 3 Bond angle restraints: 16080 Sorted by residual: angle pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 109.00 72.60 36.40 3.00e+00 1.11e-01 1.47e+02 angle pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 110.00 76.44 33.56 3.00e+00 1.11e-01 1.25e+02 angle pdb=" CB TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 109.00 77.56 31.44 3.00e+00 1.11e-01 1.10e+02 angle pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" C TYR A 205 " ideal model delta sigma weight residual 110.80 117.86 -7.06 2.13e+00 2.20e-01 1.10e+01 angle pdb=" N LEU A 102 " pdb=" CA LEU A 102 " pdb=" C LEU A 102 " ideal model delta sigma weight residual 111.02 108.23 2.79 1.22e+00 6.72e-01 5.21e+00 ... (remaining 16075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 3735 17.26 - 34.52: 337 34.52 - 51.79: 122 51.79 - 69.05: 42 69.05 - 86.31: 3 Dihedral angle restraints: 4239 sinusoidal: 2156 harmonic: 2083 Sorted by residual: dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual -180.00 -157.31 -22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -132.20 9.60 0 2.50e+00 1.60e-01 1.47e+01 dihedral pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual 122.80 131.67 -8.87 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 4236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 664 0.082 - 0.164: 26 0.164 - 0.245: 0 0.245 - 0.327: 0 0.327 - 0.409: 1 Chirality restraints: 691 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA ILE A 103 " pdb=" N ILE A 103 " pdb=" C ILE A 103 " pdb=" CB ILE A 103 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" C PRO A 132 " pdb=" CB PRO A 132 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 688 not shown) Planarity restraints: 1279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C ILE A 103 " -0.063 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 492 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C VAL A 492 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL A 492 " 0.016 2.00e-02 2.50e+03 pdb=" N SER A 493 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 102 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C LEU A 102 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU A 102 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE A 103 " 0.011 2.00e-02 2.50e+03 ... (remaining 1276 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 857 2.24 - 2.83: 19092 2.83 - 3.42: 23948 3.42 - 4.01: 32553 4.01 - 4.60: 50443 Nonbonded interactions: 126893 Sorted by model distance: nonbonded pdb="HE21 GLN A 234 " pdb=" OE1 GLN A 236 " model vdw 1.646 2.450 nonbonded pdb=" HA TYR A 205 " pdb=" HB3 TYR A 205 " model vdw 1.665 1.952 nonbonded pdb=" HH TYR A 496 " pdb=" OD2 ASP A 504 " model vdw 1.665 2.450 nonbonded pdb="HH22 ARG A 121 " pdb=" O ASN A 333 " model vdw 1.673 2.450 nonbonded pdb=" HH TYR A 162 " pdb=" O HOH A 803 " model vdw 1.699 2.450 ... (remaining 126888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 0.060 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.810 Find NCS groups from input model: 0.030 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:5.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 0.003 0.040 4552 Z= 0.140 Angle : 0.538 7.058 6212 Z= 0.285 Chirality : 0.039 0.409 691 Planarity : 0.004 0.037 752 Dihedral : 16.333 86.310 1542 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.61 % Rotamer: Outliers : 2.16 % Allowed : 20.78 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.38), residues: 544 helix: 1.66 (0.28), residues: 376 sheet: None (None), residues: 0 loop : 0.54 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 121 TYR 0.014 0.001 TYR A 84 PHE 0.017 0.001 PHE A 408 TRP 0.007 0.001 TRP A 235 HIS 0.002 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 4551) covalent geometry : angle 0.53766 / 0.28 ( 6210) SS BOND : bond 0.00303 / 0.19 ( 1) SS BOND : angle 0.72179 / 0.30 ( 2) hydrogen bonds : bond 0.11898 / 8.40 ( 295) hydrogen bonds : angle 5.07827 / 3.66 ( 849) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.135 Fit side-chains REVERT: A 100 LEU cc_start: 0.8089 (tp) cc_final: 0.7885 (tp) outliers start: 10 outliers final: 7 residues processed: 51 average time/residue: 0.4402 time to fit residues: 24.3407 Evaluate side-chains 49 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 399 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.0370 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 19 optimal weight: 0.0870 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.128548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.107261 restraints weight = 15419.535| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.70 r_work: 0.3132 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4552 Z= 0.108 Angle : 0.488 7.015 6212 Z= 0.254 Chirality : 0.039 0.407 691 Planarity : 0.004 0.034 752 Dihedral : 5.004 56.478 621 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 2.60 % Allowed : 18.40 % Favored : 79.00 % 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: 1.94 (0.38), residues: 544 helix: 1.78 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.25 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 442 TYR 0.012 0.001 TYR A 84 PHE 0.014 0.001 PHE A 408 TRP 0.007 0.001 TRP A 235 HIS 0.003 0.001 HIS A 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 4551) covalent geometry : angle 0.48774 / 0.25 ( 6210) SS BOND : bond 0.00195 / 0.12 ( 1) SS BOND : angle 0.65536 / 0.27 ( 2) hydrogen bonds : bond 0.04341 / 2.83 ( 295) hydrogen bonds : angle 4.42118 / 3.21 ( 849) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.150 Fit side-chains REVERT: A 152 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7204 (t80) REVERT: A 459 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.6864 (t80) outliers start: 12 outliers final: 3 residues processed: 52 average time/residue: 0.4797 time to fit residues: 26.8584 Evaluate side-chains 45 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.123438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.101785 restraints weight = 15520.375| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.72 r_work: 0.3086 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4552 Z= 0.177 Angle : 0.538 7.196 6212 Z= 0.283 Chirality : 0.041 0.419 691 Planarity : 0.004 0.037 752 Dihedral : 5.134 28.332 614 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.65 % Favored : 98.16 % Rotamer: Outliers : 2.16 % Allowed : 19.48 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.37), residues: 544 helix: 1.62 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.15 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 500 TYR 0.017 0.001 TYR A 84 PHE 0.014 0.001 PHE A 362 TRP 0.007 0.001 TRP A 235 HIS 0.003 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 4551) covalent geometry : angle 0.53789 / 0.28 ( 6210) SS BOND : bond 0.00258 / 0.16 ( 1) SS BOND : angle 0.70263 / 0.28 ( 2) hydrogen bonds : bond 0.05254 / 3.46 ( 295) hydrogen bonds : angle 4.60789 / 3.37 ( 849) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.237 Fit side-chains REVERT: A 152 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.7377 (t80) REVERT: A 431 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7179 (mm) REVERT: A 603 GLN cc_start: 0.7800 (mt0) cc_final: 0.6964 (mm110) outliers start: 10 outliers final: 4 residues processed: 54 average time/residue: 0.4466 time to fit residues: 26.2963 Evaluate side-chains 49 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 431 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.124110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.102637 restraints weight = 15652.784| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.72 r_work: 0.3071 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4552 Z= 0.139 Angle : 0.501 6.983 6212 Z= 0.263 Chirality : 0.040 0.412 691 Planarity : 0.004 0.039 752 Dihedral : 4.525 19.098 613 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 2.16 % Allowed : 18.83 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.37), residues: 544 helix: 1.71 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.08 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 500 TYR 0.014 0.001 TYR A 84 PHE 0.012 0.001 PHE A 362 TRP 0.007 0.001 TRP A 235 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 4551) covalent geometry : angle 0.50109 / 0.26 ( 6210) SS BOND : bond 0.00271 / 0.17 ( 1) SS BOND : angle 0.69612 / 0.29 ( 2) hydrogen bonds : bond 0.04765 / 3.11 ( 295) hydrogen bonds : angle 4.49843 / 3.28 ( 849) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.296 Fit side-chains REVERT: A 152 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.7440 (t80) REVERT: A 431 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7224 (mm) REVERT: A 603 GLN cc_start: 0.7838 (mt0) cc_final: 0.7007 (mm110) outliers start: 10 outliers final: 3 residues processed: 51 average time/residue: 0.5977 time to fit residues: 33.0509 Evaluate side-chains 47 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 431 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.120057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.098877 restraints weight = 15679.204| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.68 r_work: 0.3017 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4552 Z= 0.218 Angle : 0.569 7.106 6212 Z= 0.301 Chirality : 0.043 0.422 691 Planarity : 0.004 0.042 752 Dihedral : 5.341 30.240 613 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 1.52 % Allowed : 19.05 % Favored : 79.44 % 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: 1.54 (0.37), residues: 544 helix: 1.53 (0.27), residues: 373 sheet: None (None), residues: 0 loop : 0.01 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.019 0.001 TYR A 84 PHE 0.016 0.002 PHE A 362 TRP 0.007 0.001 TRP A 128 HIS 0.003 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 ( 4551) covalent geometry : angle 0.56921 / 0.30 ( 6210) SS BOND : bond 0.00399 / 0.25 ( 1) SS BOND : angle 0.75976 / 0.30 ( 2) hydrogen bonds : bond 0.05757 / 3.79 ( 295) hydrogen bonds : angle 4.77049 / 3.49 ( 849) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.229 Fit side-chains REVERT: A 152 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.7513 (t80) REVERT: A 603 GLN cc_start: 0.7888 (mt0) cc_final: 0.7022 (mm110) outliers start: 7 outliers final: 3 residues processed: 53 average time/residue: 0.5217 time to fit residues: 30.2317 Evaluate side-chains 47 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 377 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.122896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.101733 restraints weight = 15532.345| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.70 r_work: 0.3023 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4552 Z= 0.135 Angle : 0.497 6.725 6212 Z= 0.262 Chirality : 0.040 0.411 691 Planarity : 0.004 0.039 752 Dihedral : 4.555 18.900 613 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 1.30 % Allowed : 19.26 % Favored : 79.44 % 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: 1.77 (0.37), residues: 544 helix: 1.71 (0.27), residues: 374 sheet: None (None), residues: 0 loop : 0.08 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.014 0.001 TYR A 84 PHE 0.011 0.001 PHE A 362 TRP 0.007 0.001 TRP A 235 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 4551) covalent geometry : angle 0.49691 / 0.26 ( 6210) SS BOND : bond 0.00267 / 0.17 ( 1) SS BOND : angle 0.69365 / 0.29 ( 2) hydrogen bonds : bond 0.04796 / 3.12 ( 295) hydrogen bonds : angle 4.52424 / 3.30 ( 849) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.233 Fit side-chains REVERT: A 152 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.7472 (t80) REVERT: A 341 ARG cc_start: 0.7205 (ttm170) cc_final: 0.6928 (tmm160) REVERT: A 603 GLN cc_start: 0.7911 (mt0) cc_final: 0.7071 (mm110) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.6493 time to fit residues: 37.7110 Evaluate side-chains 50 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 377 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.123737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.102674 restraints weight = 15522.602| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.70 r_work: 0.3066 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 0.027 4552 Z= 0.125 Angle : 0.489 6.725 6212 Z= 0.257 Chirality : 0.040 0.411 691 Planarity : 0.004 0.039 752 Dihedral : 4.481 18.251 613 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 1.30 % Allowed : 19.70 % Favored : 79.00 % 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: 1.86 (0.37), residues: 544 helix: 1.78 (0.27), residues: 374 sheet: None (None), residues: 0 loop : 0.12 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 301 TYR 0.014 0.001 TYR A 84 PHE 0.010 0.001 PHE A 362 TRP 0.007 0.001 TRP A 235 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 4551) covalent geometry : angle 0.48927 / 0.26 ( 6210) SS BOND : bond 0.00219 / 0.14 ( 1) SS BOND : angle 0.63962 / 0.27 ( 2) hydrogen bonds : bond 0.04625 / 3.02 ( 295) hydrogen bonds : angle 4.46751 / 3.25 ( 849) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.223 Fit side-chains REVERT: A 152 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.7430 (t80) REVERT: A 341 ARG cc_start: 0.7240 (ttm170) cc_final: 0.6970 (tmm160) REVERT: A 603 GLN cc_start: 0.7907 (mt0) cc_final: 0.7064 (mm110) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 0.6190 time to fit residues: 34.1256 Evaluate side-chains 47 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.123448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.102407 restraints weight = 15464.200| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.69 r_work: 0.3090 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4552 Z= 0.135 Angle : 0.493 6.709 6212 Z= 0.259 Chirality : 0.040 0.413 691 Planarity : 0.004 0.039 752 Dihedral : 4.526 19.098 613 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.02 % Favored : 97.79 % Rotamer: Outliers : 1.30 % Allowed : 19.91 % Favored : 78.79 % 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: 1.86 (0.37), residues: 544 helix: 1.78 (0.27), residues: 374 sheet: None (None), residues: 0 loop : 0.10 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.015 0.001 TYR A 84 PHE 0.011 0.001 PHE A 362 TRP 0.007 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 4551) covalent geometry : angle 0.49313 / 0.26 ( 6210) SS BOND : bond 0.00239 / 0.15 ( 1) SS BOND : angle 0.66544 / 0.28 ( 2) hydrogen bonds : bond 0.04709 / 3.08 ( 295) hydrogen bonds : angle 4.47796 / 3.26 ( 849) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.222 Fit side-chains REVERT: A 152 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.7373 (t80) REVERT: A 341 ARG cc_start: 0.7150 (ttm170) cc_final: 0.6870 (tmm160) REVERT: A 603 GLN cc_start: 0.7860 (mt0) cc_final: 0.7013 (mm110) outliers start: 6 outliers final: 2 residues processed: 50 average time/residue: 0.5915 time to fit residues: 32.0555 Evaluate side-chains 46 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 256 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.125548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.104539 restraints weight = 15298.010| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.69 r_work: 0.3094 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4552 Z= 0.104 Angle : 0.471 6.534 6212 Z= 0.246 Chirality : 0.039 0.409 691 Planarity : 0.004 0.037 752 Dihedral : 4.155 15.005 613 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 1.30 % Allowed : 20.35 % Favored : 78.35 % 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: 2.03 (0.37), residues: 544 helix: 1.92 (0.27), residues: 373 sheet: None (None), residues: 0 loop : 0.14 (0.52), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 301 TYR 0.011 0.001 TYR A 84 PHE 0.009 0.001 PHE A 362 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 4551) covalent geometry : angle 0.47055 / 0.25 ( 6210) SS BOND : bond 0.00163 / 0.10 ( 1) SS BOND : angle 0.57187 / 0.25 ( 2) hydrogen bonds : bond 0.04222 / 2.74 ( 295) hydrogen bonds : angle 4.35868 / 3.17 ( 849) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.228 Fit side-chains REVERT: A 75 ASP cc_start: 0.7954 (t0) cc_final: 0.7684 (t0) REVERT: A 152 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.7266 (t80) REVERT: A 341 ARG cc_start: 0.7178 (ttm170) cc_final: 0.6919 (tmm160) REVERT: A 603 GLN cc_start: 0.7847 (mt0) cc_final: 0.7044 (mm110) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 0.5597 time to fit residues: 30.5031 Evaluate side-chains 46 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.103718 restraints weight = 15314.257| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.70 r_work: 0.3084 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4552 Z= 0.117 Angle : 0.481 6.628 6212 Z= 0.251 Chirality : 0.039 0.412 691 Planarity : 0.004 0.039 752 Dihedral : 4.280 16.456 613 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 1.08 % Allowed : 20.78 % Favored : 78.14 % 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: 1.99 (0.37), residues: 544 helix: 1.87 (0.27), residues: 376 sheet: None (None), residues: 0 loop : 0.17 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 301 TYR 0.014 0.001 TYR A 84 PHE 0.010 0.001 PHE A 362 TRP 0.007 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 4551) covalent geometry : angle 0.48100 / 0.25 ( 6210) SS BOND : bond 0.00205 / 0.13 ( 1) SS BOND : angle 0.60839 / 0.26 ( 2) hydrogen bonds : bond 0.04377 / 2.86 ( 295) hydrogen bonds : angle 4.37719 / 3.19 ( 849) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.241 Fit side-chains REVERT: A 75 ASP cc_start: 0.7972 (t0) cc_final: 0.7693 (t0) REVERT: A 152 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.7339 (t80) REVERT: A 341 ARG cc_start: 0.7260 (ttm170) cc_final: 0.6931 (tmm160) REVERT: A 603 GLN cc_start: 0.7849 (mt0) cc_final: 0.7049 (mm110) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.5424 time to fit residues: 29.0409 Evaluate side-chains 47 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.124354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.103368 restraints weight = 15250.410| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.69 r_work: 0.3079 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4552 Z= 0.124 Angle : 0.490 6.637 6212 Z= 0.255 Chirality : 0.039 0.413 691 Planarity : 0.004 0.038 752 Dihedral : 4.331 17.346 613 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 1.30 % Allowed : 20.35 % Favored : 78.35 % 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 (0.37), residues: 544 helix: 1.85 (0.27), residues: 376 sheet: None (None), residues: 0 loop : 0.16 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 301 TYR 0.014 0.001 TYR A 84 PHE 0.011 0.001 PHE A 362 TRP 0.007 0.001 TRP A 235 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 4551) covalent geometry : angle 0.49017 / 0.25 ( 6210) SS BOND : bond 0.00222 / 0.14 ( 1) SS BOND : angle 0.61705 / 0.26 ( 2) hydrogen bonds : bond 0.04472 / 2.93 ( 295) hydrogen bonds : angle 4.39489 / 3.20 ( 849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2623.28 seconds wall clock time: 45 minutes 15.25 seconds (2715.25 seconds total)