Starting phenix.real_space_refine on Thu Jul 2 13:18:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pmd_71735/07_2026/9pmd_71735.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pmd_71735/07_2026/9pmd_71735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pmd_71735/07_2026/9pmd_71735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pmd_71735/07_2026/9pmd_71735.map" model { file = "/net/cci-nas-00/data/ceres_data/9pmd_71735/07_2026/9pmd_71735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pmd_71735/07_2026/9pmd_71735.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 27 5.16 5 Na 1 4.78 5 C 2761 2.51 5 N 673 2.21 5 O 731 1.98 5 H 4242 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 8435 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 8432 Classifications: {'peptide': 528} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 502} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 2 Ad-hoc single atom residues: {' NA': 1} Classifications: {'water': 2} Link IDs: {None: 1} Chain breaks: 1 Time building chain proxies: 1.36, per 1000 atoms: 0.16 Number of scatterers: 8435 At special positions: 0 Unit cell: (112.88, 71.38, 69.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 Na 1 11.00 O 731 8.00 N 673 7.00 C 2761 6.00 H 4242 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 136 " 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: 0.68 Conformation dependent library (CDL) restraints added in 200.2 milliseconds 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 982 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 2 sheets defined 78.0% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 9 through 12 Processing helix chain 'A' and resid 15 through 28 Processing helix chain 'A' and resid 29 through 37 removed outlier: 3.677A pdb=" N PHE A 34 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 36 " --> pdb=" O ASN A 32 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU A 37 " --> pdb=" O GLY A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 59 through 64 removed outlier: 3.528A pdb=" N ASN A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.612A pdb=" N PHE A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 140 through 168 removed outlier: 3.537A pdb=" N LEU A 144 " --> pdb=" O TRP A 140 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLN A 162 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 187 Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 192 through 222 removed outlier: 3.715A pdb=" N ALA A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.647A pdb=" N ILE A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 253 Proline residue: A 247 - end of helix removed outlier: 3.801A pdb=" N PHE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 270 Proline residue: A 266 - end of helix removed outlier: 3.769A pdb=" N LEU A 269 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 removed outlier: 4.082A pdb=" N TRP A 275 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 289 through 305 Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 337 through 364 Processing helix chain 'A' and resid 365 through 368 Processing helix chain 'A' and resid 371 through 382 Processing helix chain 'A' and resid 382 through 397 Processing helix chain 'A' and resid 398 through 416 removed outlier: 3.557A pdb=" N PHE A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 421 through 424 Processing helix chain 'A' and resid 425 through 454 removed outlier: 4.158A pdb=" N THR A 429 " --> pdb=" O TYR A 425 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR A 447 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 483 Proline residue: A 478 - end of helix removed outlier: 3.734A pdb=" N VAL A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 483 " --> pdb=" O TYR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 489 through 507 removed outlier: 3.669A pdb=" N LEU A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84 259 hydrogen bonds defined for protein. 726 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: 1.62 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4239 1.04 - 1.23: 63 1.23 - 1.43: 1767 1.43 - 1.63: 2428 1.63 - 1.82: 47 Bond restraints: 8544 Sorted by residual: bond pdb=" CB LYS A 325 " pdb=" CG LYS A 325 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.74e-01 bond pdb=" CB GLN A 107 " pdb=" CG GLN A 107 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.20e-01 bond pdb=" C VAL A 198 " pdb=" O VAL A 198 " ideal model delta sigma weight residual 1.237 1.246 -0.009 1.17e-02 7.31e+03 6.10e-01 bond pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " ideal model delta sigma weight residual 1.808 1.783 0.025 3.30e-02 9.18e+02 5.90e-01 bond pdb=" CG LYS A 325 " pdb=" CD LYS A 325 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 4.70e-01 ... (remaining 8539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 15009 1.46 - 2.92: 397 2.92 - 4.37: 35 4.37 - 5.83: 4 5.83 - 7.29: 1 Bond angle restraints: 15446 Sorted by residual: angle pdb=" CB LYS A 325 " pdb=" CG LYS A 325 " pdb=" CD LYS A 325 " ideal model delta sigma weight residual 111.30 118.59 -7.29 2.30e+00 1.89e-01 1.00e+01 angle pdb=" CA LYS A 325 " pdb=" CB LYS A 325 " pdb=" CG LYS A 325 " ideal model delta sigma weight residual 114.10 119.07 -4.97 2.00e+00 2.50e-01 6.17e+00 angle pdb=" CA CYS A 50 " pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " ideal model delta sigma weight residual 114.40 119.11 -4.71 2.30e+00 1.89e-01 4.19e+00 angle pdb=" CB GLN A 107 " pdb=" CG GLN A 107 " pdb=" CD GLN A 107 " ideal model delta sigma weight residual 112.60 116.08 -3.48 1.70e+00 3.46e-01 4.19e+00 angle pdb=" N TYR A 396 " pdb=" CA TYR A 396 " pdb=" C TYR A 396 " ideal model delta sigma weight residual 114.39 117.22 -2.83 1.45e+00 4.76e-01 3.80e+00 ... (remaining 15441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 3610 16.82 - 33.64: 276 33.64 - 50.45: 84 50.45 - 67.27: 54 67.27 - 84.09: 11 Dihedral angle restraints: 4035 sinusoidal: 2144 harmonic: 1891 Sorted by residual: dihedral pdb=" CA CYS A 50 " pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 113 " ideal model delta sinusoidal sigma weight residual -73.00 -4.11 -68.89 1 2.00e+01 2.50e-03 1.54e+01 dihedral pdb=" CG ARG A 49 " pdb=" CD ARG A 49 " pdb=" NE ARG A 49 " pdb=" CZ ARG A 49 " ideal model delta sinusoidal sigma weight residual 180.00 138.03 41.97 2 1.50e+01 4.44e-03 9.54e+00 dihedral pdb=" CB MET A 445 " pdb=" CG MET A 445 " pdb=" SD MET A 445 " pdb=" CE MET A 445 " ideal model delta sinusoidal sigma weight residual -180.00 -120.31 -59.69 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 528 0.044 - 0.087: 120 0.087 - 0.131: 23 0.131 - 0.174: 1 0.174 - 0.218: 1 Chirality restraints: 673 Sorted by residual: chirality pdb=" CA TRP A 275 " pdb=" N TRP A 275 " pdb=" C TRP A 275 " pdb=" CB TRP A 275 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB VAL A 197 " pdb=" CA VAL A 197 " pdb=" CG1 VAL A 197 " pdb=" CG2 VAL A 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE A 277 " pdb=" N ILE A 277 " pdb=" C ILE A 277 " pdb=" CB ILE A 277 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 670 not shown) Planarity restraints: 1228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 207 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C GLN A 207 " 0.036 2.00e-02 2.50e+03 pdb=" O GLN A 207 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 208 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 205 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C MET A 205 " -0.030 2.00e-02 2.50e+03 pdb=" O MET A 205 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY A 206 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 358 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C TYR A 358 " 0.029 2.00e-02 2.50e+03 pdb=" O TYR A 358 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE A 359 " -0.010 2.00e-02 2.50e+03 ... (remaining 1225 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 404 2.19 - 2.79: 16653 2.79 - 3.39: 23600 3.39 - 4.00: 29937 4.00 - 4.60: 46909 Nonbonded interactions: 117503 Sorted by model distance: nonbonded pdb=" OD1 ASP A 165 " pdb="HH12 ARG A 169 " model vdw 1.584 2.450 nonbonded pdb=" OE1 GLN A 180 " pdb="HD22 ASN A 210 " model vdw 1.636 2.450 nonbonded pdb=" OE1 GLU A 13 " pdb=" HG SER A 225 " model vdw 1.649 2.450 nonbonded pdb=" O ASP A 371 " pdb="HD21 ASN A 375 " model vdw 1.670 2.450 nonbonded pdb=" OD2 ASP A 364 " pdb=" HH TYR A 492 " model vdw 1.684 2.450 ... (remaining 117498 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: 2.400 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: 0.050 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.880 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4304 Z= 0.113 Angle : 0.570 7.288 5861 Z= 0.316 Chirality : 0.039 0.218 673 Planarity : 0.007 0.054 726 Dihedral : 13.831 81.298 1524 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.87 % Allowed : 14.38 % Favored : 84.75 % 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: 1.70 (0.38), residues: 526 helix: 1.48 (0.30), residues: 318 sheet: None (None), residues: 0 loop : 0.76 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.003 ARG A 254 TYR 0.013 0.004 TYR A 396 PHE 0.008 0.001 PHE A 200 TRP 0.010 0.001 TRP A 256 HIS 0.002 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 4302) covalent geometry : angle 0.56639 / 0.31 ( 5857) SS BOND : bond 0.00271 / 0.13 ( 2) SS BOND : angle 2.43489 / 1.35 ( 4) hydrogen bonds : bond 0.15821 / 10.27 ( 259) hydrogen bonds : angle 5.28880 / 3.61 ( 726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8190 (mm-30) REVERT: A 62 TRP cc_start: 0.8498 (m100) cc_final: 0.8097 (m100) REVERT: A 191 LYS cc_start: 0.8544 (mttt) cc_final: 0.8340 (mttm) REVERT: A 325 LYS cc_start: 0.9170 (tppp) cc_final: 0.8832 (ptpt) REVERT: A 326 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8619 (mm-40) outliers start: 4 outliers final: 1 residues processed: 60 average time/residue: 0.7151 time to fit residues: 44.8441 Evaluate side-chains 50 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.084985 restraints weight = 21359.000| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.39 r_work: 0.2878 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4304 Z= 0.132 Angle : 0.517 5.521 5861 Z= 0.273 Chirality : 0.037 0.119 673 Planarity : 0.004 0.036 726 Dihedral : 3.467 15.594 576 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.96 % Allowed : 12.85 % Favored : 85.19 % 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 are not related in a simple way. whole: 1.87 (0.38), residues: 526 helix: 1.65 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.67 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.008 0.001 TYR A 447 PHE 0.011 0.001 PHE A 34 TRP 0.010 0.001 TRP A 256 HIS 0.002 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 4302) covalent geometry : angle 0.51491 / 0.27 ( 5857) SS BOND : bond 0.00141 / 0.07 ( 2) SS BOND : angle 1.74819 / 0.92 ( 4) hydrogen bonds : bond 0.05107 / 3.21 ( 259) hydrogen bonds : angle 4.35947 / 3.02 ( 726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8543 (t80) REVERT: A 325 LYS cc_start: 0.9152 (tppp) cc_final: 0.8841 (ptmt) REVERT: A 326 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8583 (tp-100) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 0.7177 time to fit residues: 45.1658 Evaluate side-chains 54 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 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 = 0.3266 r_free = 0.3266 target = 0.102846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.083798 restraints weight = 21286.498| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.38 r_work: 0.2850 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4304 Z= 0.133 Angle : 0.488 4.852 5861 Z= 0.257 Chirality : 0.037 0.122 673 Planarity : 0.005 0.090 726 Dihedral : 3.553 16.018 576 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.96 % Allowed : 12.85 % Favored : 85.19 % 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 are not related in a simple way. whole: 2.06 (0.37), residues: 526 helix: 1.83 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.65 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 488 TYR 0.008 0.001 TYR A 239 PHE 0.011 0.001 PHE A 34 TRP 0.011 0.001 TRP A 256 HIS 0.003 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 4302) covalent geometry : angle 0.48623 / 0.26 ( 5857) SS BOND : bond 0.00125 / 0.06 ( 2) SS BOND : angle 1.62158 / 0.85 ( 4) hydrogen bonds : bond 0.04776 / 3.01 ( 259) hydrogen bonds : angle 4.16486 / 2.89 ( 726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8574 (t80) REVERT: A 325 LYS cc_start: 0.9140 (tppp) cc_final: 0.8827 (ptmt) outliers start: 9 outliers final: 2 residues processed: 57 average time/residue: 0.8017 time to fit residues: 47.7098 Evaluate side-chains 54 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.104499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.084739 restraints weight = 21473.990| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.44 r_work: 0.2870 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4304 Z= 0.122 Angle : 0.481 4.859 5861 Z= 0.251 Chirality : 0.037 0.123 673 Planarity : 0.004 0.044 726 Dihedral : 3.505 16.762 576 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.31 % Allowed : 14.16 % Favored : 84.53 % 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 are not related in a simple way. whole: 2.19 (0.38), residues: 526 helix: 1.95 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.69 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 488 TYR 0.008 0.001 TYR A 447 PHE 0.012 0.001 PHE A 34 TRP 0.010 0.001 TRP A 256 HIS 0.001 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 4302) covalent geometry : angle 0.47971 / 0.25 ( 5857) SS BOND : bond 0.00167 / 0.08 ( 2) SS BOND : angle 1.60896 / 0.85 ( 4) hydrogen bonds : bond 0.04458 / 2.80 ( 259) hydrogen bonds : angle 4.05619 / 2.81 ( 726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8720 (t80) REVERT: A 325 LYS cc_start: 0.9105 (tppp) cc_final: 0.8853 (ptmt) outliers start: 6 outliers final: 2 residues processed: 57 average time/residue: 0.7474 time to fit residues: 44.6176 Evaluate side-chains 53 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3298 r_free = 0.3298 target = 0.104784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.085056 restraints weight = 21235.891| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.43 r_work: 0.2873 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4304 Z= 0.116 Angle : 0.465 4.834 5861 Z= 0.243 Chirality : 0.037 0.132 673 Planarity : 0.003 0.039 726 Dihedral : 3.469 16.985 576 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.53 % Allowed : 14.81 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.38), residues: 526 helix: 2.03 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.70 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 488 TYR 0.007 0.001 TYR A 239 PHE 0.011 0.001 PHE A 34 TRP 0.009 0.001 TRP A 256 HIS 0.001 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 4302) covalent geometry : angle 0.46372 / 0.24 ( 5857) SS BOND : bond 0.00083 / 0.04 ( 2) SS BOND : angle 1.55378 / 0.82 ( 4) hydrogen bonds : bond 0.04311 / 2.70 ( 259) hydrogen bonds : angle 3.98083 / 2.76 ( 726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8725 (t80) REVERT: A 325 LYS cc_start: 0.9091 (tppp) cc_final: 0.8846 (ptpt) outliers start: 7 outliers final: 3 residues processed: 56 average time/residue: 0.6318 time to fit residues: 37.4379 Evaluate side-chains 52 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3280 r_free = 0.3280 target = 0.103227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.083576 restraints weight = 21241.658| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.40 r_work: 0.2847 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4304 Z= 0.156 Angle : 0.485 4.951 5861 Z= 0.256 Chirality : 0.038 0.151 673 Planarity : 0.003 0.032 726 Dihedral : 3.534 17.471 576 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.53 % Allowed : 15.47 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.37), residues: 526 helix: 1.93 (0.28), residues: 338 sheet: None (None), residues: 0 loop : 0.57 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 82 TYR 0.008 0.001 TYR A 447 PHE 0.012 0.001 PHE A 34 TRP 0.009 0.001 TRP A 256 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 4302) covalent geometry : angle 0.48334 / 0.26 ( 5857) SS BOND : bond 0.00147 / 0.07 ( 2) SS BOND : angle 1.64052 / 0.87 ( 4) hydrogen bonds : bond 0.04742 / 2.98 ( 259) hydrogen bonds : angle 4.04505 / 2.80 ( 726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8810 (t80) outliers start: 7 outliers final: 3 residues processed: 53 average time/residue: 0.6889 time to fit residues: 38.5216 Evaluate side-chains 51 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 347 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3288 r_free = 0.3288 target = 0.103651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.084076 restraints weight = 21547.727| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.38 r_work: 0.2863 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4304 Z= 0.136 Angle : 0.498 7.278 5861 Z= 0.257 Chirality : 0.037 0.162 673 Planarity : 0.003 0.029 726 Dihedral : 3.470 17.413 575 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.74 % Allowed : 15.90 % Favored : 82.35 % 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: 2.16 (0.37), residues: 526 helix: 1.98 (0.28), residues: 338 sheet: None (None), residues: 0 loop : 0.54 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 82 TYR 0.008 0.001 TYR A 239 PHE 0.012 0.001 PHE A 34 TRP 0.009 0.001 TRP A 256 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 4302) covalent geometry : angle 0.49606 / 0.26 ( 5857) SS BOND : bond 0.00111 / 0.05 ( 2) SS BOND : angle 1.60138 / 0.84 ( 4) hydrogen bonds : bond 0.04541 / 2.85 ( 259) hydrogen bonds : angle 3.99371 / 2.77 ( 726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8835 (t80) REVERT: A 325 LYS cc_start: 0.9016 (tppp) cc_final: 0.8768 (ptmt) outliers start: 8 outliers final: 4 residues processed: 55 average time/residue: 0.6691 time to fit residues: 38.7803 Evaluate side-chains 51 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.084495 restraints weight = 21274.115| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.40 r_work: 0.2868 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 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 : 0.003 0.025 4304 Z= 0.129 Angle : 0.486 6.399 5861 Z= 0.252 Chirality : 0.037 0.172 673 Planarity : 0.003 0.029 726 Dihedral : 3.452 17.363 575 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.53 % Allowed : 15.90 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.37), residues: 526 helix: 2.01 (0.28), residues: 338 sheet: None (None), residues: 0 loop : 0.55 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 82 TYR 0.008 0.001 TYR A 447 PHE 0.011 0.001 PHE A 34 TRP 0.011 0.001 TRP A 62 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 4302) covalent geometry : angle 0.48432 / 0.25 ( 5857) SS BOND : bond 0.00081 / 0.04 ( 2) SS BOND : angle 1.56491 / 0.83 ( 4) hydrogen bonds : bond 0.04441 / 2.78 ( 259) hydrogen bonds : angle 3.96612 / 2.75 ( 726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8801 (t80) outliers start: 7 outliers final: 4 residues processed: 55 average time/residue: 0.7056 time to fit residues: 40.8477 Evaluate side-chains 53 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.104680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.085405 restraints weight = 21196.360| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.37 r_work: 0.2867 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4304 Z= 0.117 Angle : 0.483 6.997 5861 Z= 0.250 Chirality : 0.037 0.179 673 Planarity : 0.003 0.028 726 Dihedral : 3.420 17.319 575 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.53 % Allowed : 16.34 % Favored : 82.14 % 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: 2.27 (0.37), residues: 526 helix: 2.05 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.61 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 82 TYR 0.007 0.001 TYR A 239 PHE 0.011 0.001 PHE A 34 TRP 0.012 0.001 TRP A 62 HIS 0.001 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 4302) covalent geometry : angle 0.48192 / 0.25 ( 5857) SS BOND : bond 0.00070 / 0.03 ( 2) SS BOND : angle 1.56800 / 0.83 ( 4) hydrogen bonds : bond 0.04268 / 2.67 ( 259) hydrogen bonds : angle 3.92335 / 2.73 ( 726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8769 (t80) outliers start: 7 outliers final: 5 residues processed: 57 average time/residue: 0.6838 time to fit residues: 41.1913 Evaluate side-chains 55 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.0670 chunk 44 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.1980 chunk 3 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.105686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.086192 restraints weight = 21316.597| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.42 r_work: 0.2881 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4304 Z= 0.101 Angle : 0.477 7.260 5861 Z= 0.245 Chirality : 0.037 0.186 673 Planarity : 0.003 0.027 726 Dihedral : 3.360 17.201 575 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.87 % Allowed : 16.99 % Favored : 82.14 % 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: 2.40 (0.38), residues: 526 helix: 2.16 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.66 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 82 TYR 0.008 0.001 TYR A 447 PHE 0.010 0.001 PHE A 34 TRP 0.019 0.001 TRP A 62 HIS 0.001 0.000 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 4302) covalent geometry : angle 0.47596 / 0.24 ( 5857) SS BOND : bond 0.00011 / 0.01 ( 2) SS BOND : angle 1.52501 / 0.80 ( 4) hydrogen bonds : bond 0.03947 / 2.47 ( 259) hydrogen bonds : angle 3.84706 / 2.68 ( 726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8698 (t80) REVERT: A 271 VAL cc_start: 0.8224 (t) cc_final: 0.8003 (p) outliers start: 4 outliers final: 3 residues processed: 58 average time/residue: 0.7467 time to fit residues: 45.6719 Evaluate side-chains 54 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.105777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.086252 restraints weight = 21109.891| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.37 r_work: 0.2881 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4304 Z= 0.113 Angle : 0.488 7.485 5861 Z= 0.251 Chirality : 0.037 0.174 673 Planarity : 0.003 0.034 726 Dihedral : 3.346 17.337 575 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.09 % Allowed : 16.99 % 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 are not related in a simple way. whole: 2.45 (0.38), residues: 526 helix: 2.17 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.75 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 82 TYR 0.006 0.001 TYR A 239 PHE 0.010 0.001 PHE A 34 TRP 0.021 0.001 TRP A 62 HIS 0.002 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 4302) covalent geometry : angle 0.48516 / 0.25 ( 5857) SS BOND : bond 0.00051 / 0.02 ( 2) SS BOND : angle 2.06276 / 1.04 ( 4) hydrogen bonds : bond 0.04045 / 2.53 ( 259) hydrogen bonds : angle 3.85653 / 2.68 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2533.12 seconds wall clock time: 43 minutes 31.08 seconds (2611.08 seconds total)