Starting phenix.real_space_refine on Tue Mar 3 12:45:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yim_33861/03_2026/7yim_33861.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yim_33861/03_2026/7yim_33861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yim_33861/03_2026/7yim_33861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yim_33861/03_2026/7yim_33861.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yim_33861/03_2026/7yim_33861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yim_33861/03_2026/7yim_33861.map" } resolution = 2.6 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= -0.006 sd= 0.095 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 2925 2.51 5 N 791 2.21 5 O 901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4657 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4657 Classifications: {'peptide': 592} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 570} Time building chain proxies: 0.89, per 1000 atoms: 0.19 Number of scatterers: 4657 At special positions: 0 Unit cell: (69.5594, 91.3616, 103.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 901 8.00 N 791 7.00 C 2925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 114 " distance=2.02 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 124 " distance=2.02 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 270 " distance=2.01 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.00 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 313 " distance=2.04 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 393 " distance=2.02 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 462 " distance=2.01 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 472 " distance=2.01 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 501 " distance=2.01 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 511 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " 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: 0.36 Conformation dependent library (CDL) restraints added in 358.2 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 75.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 removed outlier: 4.209A pdb=" N ASP A 33 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.750A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 75 removed outlier: 3.573A pdb=" N GLU A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 101 through 108 removed outlier: 3.546A pdb=" N LEU A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.613A pdb=" N SER A 115 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 116 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.629A pdb=" N ASP A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 168 Processing helix chain 'A' and resid 174 through 193 Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 197 through 231 removed outlier: 3.915A pdb=" N THR A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 247 Processing helix chain 'A' and resid 251 through 271 Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 301 through 305 removed outlier: 4.018A pdb=" N LEU A 305 " --> pdb=" O CYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 343 through 361 Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.746A pdb=" N PHE A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 removed outlier: 4.181A pdb=" N CYS A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 439 removed outlier: 7.982A pdb=" N GLU A 424 " --> pdb=" O GLN A 420 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N TYR A 425 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 462 Processing helix chain 'A' and resid 467 through 491 removed outlier: 4.204A pdb=" N ALA A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 removed outlier: 3.527A pdb=" N GLY A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 514 Processing helix chain 'A' and resid 527 through 531 removed outlier: 3.999A pdb=" N LYS A 530 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 560 Processing helix chain 'A' and resid 565 through 582 Processing helix chain 'A' and resid 587 through 608 removed outlier: 3.913A pdb=" N CYS A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1072 1.33 - 1.46: 1193 1.46 - 1.58: 2428 1.58 - 1.71: 0 1.71 - 1.84: 48 Bond restraints: 4741 Sorted by residual: bond pdb=" CB VAL A 355 " pdb=" CG2 VAL A 355 " ideal model delta sigma weight residual 1.521 1.408 0.113 3.30e-02 9.18e+02 1.17e+01 bond pdb=" C TYR A 174 " pdb=" N ALA A 175 " ideal model delta sigma weight residual 1.332 1.297 0.035 1.09e-02 8.42e+03 1.04e+01 bond pdb=" CG GLN A 245 " pdb=" CD GLN A 245 " ideal model delta sigma weight residual 1.516 1.439 0.077 2.50e-02 1.60e+03 9.56e+00 bond pdb=" CB GLN A 245 " pdb=" CG GLN A 245 " ideal model delta sigma weight residual 1.520 1.427 0.093 3.00e-02 1.11e+03 9.55e+00 bond pdb=" CG1 ILE A 314 " pdb=" CD1 ILE A 314 " ideal model delta sigma weight residual 1.513 1.400 0.113 3.90e-02 6.57e+02 8.40e+00 ... (remaining 4736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 6228 2.87 - 5.74: 147 5.74 - 8.61: 23 8.61 - 11.48: 1 11.48 - 14.36: 1 Bond angle restraints: 6400 Sorted by residual: angle pdb=" CA CYS A 591 " pdb=" CB CYS A 591 " pdb=" SG CYS A 591 " ideal model delta sigma weight residual 114.40 128.76 -14.36 2.30e+00 1.89e-01 3.90e+01 angle pdb=" C CYS A 591 " pdb=" CA CYS A 591 " pdb=" CB CYS A 591 " ideal model delta sigma weight residual 110.88 103.82 7.06 1.57e+00 4.06e-01 2.02e+01 angle pdb=" CA GLU A 81 " pdb=" CB GLU A 81 " pdb=" CG GLU A 81 " ideal model delta sigma weight residual 114.10 122.78 -8.68 2.00e+00 2.50e-01 1.88e+01 angle pdb=" C GLU A 398 " pdb=" N GLU A 399 " pdb=" CA GLU A 399 " ideal model delta sigma weight residual 122.60 116.29 6.31 1.56e+00 4.11e-01 1.64e+01 angle pdb=" C LYS A 581 " pdb=" N CYS A 582 " pdb=" CA CYS A 582 " ideal model delta sigma weight residual 122.54 115.64 6.90 1.82e+00 3.02e-01 1.44e+01 ... (remaining 6395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 2536 17.11 - 34.21: 342 34.21 - 51.31: 60 51.31 - 68.42: 19 68.42 - 85.52: 5 Dihedral angle restraints: 2962 sinusoidal: 1222 harmonic: 1740 Sorted by residual: dihedral pdb=" CB CYS A 582 " pdb=" SG CYS A 582 " pdb=" SG CYS A 591 " pdb=" CB CYS A 591 " ideal model delta sinusoidal sigma weight residual 93.00 173.66 -80.66 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CA LYS A 76 " pdb=" C LYS A 76 " pdb=" N PRO A 77 " pdb=" CA PRO A 77 " ideal model delta harmonic sigma weight residual -180.00 -144.61 -35.39 0 5.00e+00 4.00e-02 5.01e+01 dihedral pdb=" CA SER A 117 " pdb=" C SER A 117 " pdb=" N GLU A 118 " pdb=" CA GLU A 118 " ideal model delta harmonic sigma weight residual -180.00 -146.39 -33.61 0 5.00e+00 4.00e-02 4.52e+01 ... (remaining 2959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 519 0.070 - 0.139: 176 0.139 - 0.209: 19 0.209 - 0.278: 4 0.278 - 0.348: 1 Chirality restraints: 719 Sorted by residual: chirality pdb=" CB ILE A 481 " pdb=" CA ILE A 481 " pdb=" CG1 ILE A 481 " pdb=" CG2 ILE A 481 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB VAL A 355 " pdb=" CA VAL A 355 " pdb=" CG1 VAL A 355 " pdb=" CG2 VAL A 355 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA PRO A 510 " pdb=" N PRO A 510 " pdb=" C PRO A 510 " pdb=" CB PRO A 510 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 716 not shown) Planarity restraints: 837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 509 " 0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO A 510 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 592 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C PHE A 592 " 0.047 2.00e-02 2.50e+03 pdb=" O PHE A 592 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 593 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 175 " 0.045 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO A 176 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.038 5.00e-02 4.00e+02 ... (remaining 834 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1194 2.80 - 3.32: 4406 3.32 - 3.85: 7985 3.85 - 4.37: 9276 4.37 - 4.90: 15248 Nonbonded interactions: 38109 Sorted by model distance: nonbonded pdb=" OE1 GLU A 165 " pdb=" NH1 ARG A 169 " model vdw 2.272 3.120 nonbonded pdb=" O ARG A 509 " pdb=" OG SER A 513 " model vdw 2.276 3.040 nonbonded pdb=" OE1 GLU A 62 " pdb=" OH TYR A 108 " model vdw 2.284 3.040 nonbonded pdb=" OG SER A 42 " pdb=" OD2 ASP A 45 " model vdw 2.294 3.040 nonbonded pdb=" O ALA A 44 " pdb=" OG1 THR A 48 " model vdw 2.311 3.040 ... (remaining 38104 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.410 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:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 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 : 0.013 0.113 4757 Z= 0.530 Angle : 1.155 14.355 6432 Z= 0.642 Chirality : 0.068 0.348 719 Planarity : 0.009 0.089 837 Dihedral : 15.893 85.522 1782 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.78 % Allowed : 6.59 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.18 % 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: -4.17 (0.25), residues: 590 helix: -2.57 (0.18), residues: 420 sheet: None (None), residues: 0 loop : -2.74 (0.38), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 509 TYR 0.043 0.005 TYR A 185 PHE 0.031 0.005 PHE A 235 TRP 0.020 0.007 TRP A 181 HIS 0.012 0.003 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.01290 ( 4741) covalent geometry : angle 1.13553 ( 6400) SS BOND : bond 0.01411 ( 16) SS BOND : angle 3.19771 ( 32) hydrogen bonds : bond 0.13229 ( 312) hydrogen bonds : angle 6.74957 ( 924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 519 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6959 (tm-30) outliers start: 4 outliers final: 0 residues processed: 68 average time/residue: 0.8020 time to fit residues: 56.1319 Evaluate side-chains 37 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 220 ASN A 389 ASN A 420 GLN A 534 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.205827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.161743 restraints weight = 5384.104| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 2.40 r_work: 0.4252 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4757 Z= 0.139 Angle : 0.582 6.746 6432 Z= 0.314 Chirality : 0.040 0.159 719 Planarity : 0.005 0.052 837 Dihedral : 5.329 30.419 631 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.16 % Allowed : 13.37 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.60 (0.31), residues: 590 helix: -0.46 (0.23), residues: 429 sheet: None (None), residues: 0 loop : -2.46 (0.42), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 168 TYR 0.019 0.002 TYR A 185 PHE 0.016 0.002 PHE A 235 TRP 0.010 0.003 TRP A 181 HIS 0.007 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 4741) covalent geometry : angle 0.57182 ( 6400) SS BOND : bond 0.00320 ( 16) SS BOND : angle 1.62273 ( 32) hydrogen bonds : bond 0.04497 ( 312) hydrogen bonds : angle 4.69138 ( 924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7017 (tp) cc_final: 0.6786 (tp) REVERT: A 228 LYS cc_start: 0.7667 (tttt) cc_final: 0.7063 (mppt) REVERT: A 548 MET cc_start: 0.6262 (mtp) cc_final: 0.6040 (tpt) outliers start: 6 outliers final: 1 residues processed: 63 average time/residue: 0.6112 time to fit residues: 39.8723 Evaluate side-chains 45 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 9 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.202127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.157930 restraints weight = 5358.345| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 2.41 r_work: 0.4187 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4757 Z= 0.182 Angle : 0.622 8.778 6432 Z= 0.327 Chirality : 0.043 0.151 719 Planarity : 0.005 0.046 837 Dihedral : 5.042 27.518 631 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.52 % Allowed : 15.12 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.32), residues: 590 helix: 0.08 (0.23), residues: 429 sheet: None (None), residues: 0 loop : -2.19 (0.45), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 332 TYR 0.018 0.002 TYR A 164 PHE 0.025 0.002 PHE A 50 TRP 0.007 0.002 TRP A 181 HIS 0.007 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 4741) covalent geometry : angle 0.61674 ( 6400) SS BOND : bond 0.00433 ( 16) SS BOND : angle 1.25907 ( 32) hydrogen bonds : bond 0.05046 ( 312) hydrogen bonds : angle 4.66431 ( 924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7070 (tp) cc_final: 0.6792 (tp) REVERT: A 228 LYS cc_start: 0.7911 (tttt) cc_final: 0.7309 (mppt) outliers start: 13 outliers final: 5 residues processed: 55 average time/residue: 0.4787 time to fit residues: 27.5680 Evaluate side-chains 43 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.206313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.161253 restraints weight = 5394.330| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 2.43 r_work: 0.4248 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4757 Z= 0.134 Angle : 0.560 7.537 6432 Z= 0.298 Chirality : 0.040 0.134 719 Planarity : 0.004 0.037 837 Dihedral : 4.647 23.759 631 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.10 % Allowed : 16.47 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.33), residues: 590 helix: 0.69 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -2.10 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 332 TYR 0.016 0.001 TYR A 164 PHE 0.033 0.002 PHE A 50 TRP 0.005 0.002 TRP A 181 HIS 0.006 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4741) covalent geometry : angle 0.55313 ( 6400) SS BOND : bond 0.00414 ( 16) SS BOND : angle 1.39617 ( 32) hydrogen bonds : bond 0.04284 ( 312) hydrogen bonds : angle 4.37785 ( 924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7102 (tp) cc_final: 0.6858 (tp) REVERT: A 228 LYS cc_start: 0.7758 (tttt) cc_final: 0.7077 (mppt) REVERT: A 448 MET cc_start: 0.6748 (mtp) cc_final: 0.6294 (mtt) outliers start: 16 outliers final: 6 residues processed: 59 average time/residue: 0.4648 time to fit residues: 28.7620 Evaluate side-chains 45 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 122 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.202051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.156380 restraints weight = 5383.295| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 2.41 r_work: 0.4181 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4757 Z= 0.192 Angle : 0.627 8.427 6432 Z= 0.331 Chirality : 0.044 0.140 719 Planarity : 0.004 0.041 837 Dihedral : 4.791 22.938 631 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.52 % Allowed : 18.41 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.33), residues: 590 helix: 0.50 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -2.08 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 332 TYR 0.015 0.002 TYR A 185 PHE 0.036 0.003 PHE A 50 TRP 0.006 0.002 TRP A 181 HIS 0.007 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 4741) covalent geometry : angle 0.61831 ( 6400) SS BOND : bond 0.00531 ( 16) SS BOND : angle 1.63319 ( 32) hydrogen bonds : bond 0.04976 ( 312) hydrogen bonds : angle 4.59286 ( 924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7101 (tp) cc_final: 0.6839 (tp) REVERT: A 124 CYS cc_start: 0.6451 (t) cc_final: 0.5932 (t) REVERT: A 228 LYS cc_start: 0.7843 (tttt) cc_final: 0.7176 (mppt) REVERT: A 448 MET cc_start: 0.6871 (mtp) cc_final: 0.6318 (mtt) REVERT: A 530 LYS cc_start: 0.5852 (mtmt) cc_final: 0.5467 (mtmp) outliers start: 13 outliers final: 6 residues processed: 55 average time/residue: 0.5179 time to fit residues: 29.8424 Evaluate side-chains 44 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.205072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.159576 restraints weight = 5436.518| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 2.45 r_work: 0.4208 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4757 Z= 0.131 Angle : 0.551 8.322 6432 Z= 0.297 Chirality : 0.040 0.133 719 Planarity : 0.004 0.035 837 Dihedral : 4.470 21.335 631 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.74 % Allowed : 20.35 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.34), residues: 590 helix: 0.93 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -1.93 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 332 TYR 0.017 0.001 TYR A 164 PHE 0.024 0.002 PHE A 54 TRP 0.006 0.002 TRP A 181 HIS 0.006 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4741) covalent geometry : angle 0.54554 ( 6400) SS BOND : bond 0.00324 ( 16) SS BOND : angle 1.25042 ( 32) hydrogen bonds : bond 0.04166 ( 312) hydrogen bonds : angle 4.31358 ( 924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7099 (tp) cc_final: 0.6849 (tp) REVERT: A 228 LYS cc_start: 0.7801 (tttt) cc_final: 0.7081 (mppt) REVERT: A 403 LYS cc_start: 0.6547 (pttt) cc_final: 0.5844 (tptp) REVERT: A 448 MET cc_start: 0.7011 (mtp) cc_final: 0.6605 (mtt) REVERT: A 530 LYS cc_start: 0.5732 (mtmt) cc_final: 0.5332 (mtmp) outliers start: 9 outliers final: 4 residues processed: 49 average time/residue: 0.5265 time to fit residues: 27.0101 Evaluate side-chains 43 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 54 optimal weight: 0.0980 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.206457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.161695 restraints weight = 5384.429| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 2.42 r_work: 0.4247 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4757 Z= 0.126 Angle : 0.545 9.297 6432 Z= 0.292 Chirality : 0.040 0.128 719 Planarity : 0.004 0.034 837 Dihedral : 4.337 21.820 631 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.13 % Allowed : 21.12 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.34), residues: 590 helix: 1.10 (0.24), residues: 433 sheet: None (None), residues: 0 loop : -1.64 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 169 TYR 0.008 0.001 TYR A 505 PHE 0.030 0.002 PHE A 54 TRP 0.007 0.002 TRP A 181 HIS 0.008 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 4741) covalent geometry : angle 0.53985 ( 6400) SS BOND : bond 0.00290 ( 16) SS BOND : angle 1.15504 ( 32) hydrogen bonds : bond 0.04041 ( 312) hydrogen bonds : angle 4.22300 ( 924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7109 (tp) cc_final: 0.6854 (tp) REVERT: A 124 CYS cc_start: 0.6495 (t) cc_final: 0.6038 (t) REVERT: A 228 LYS cc_start: 0.7798 (tttt) cc_final: 0.7119 (mppt) REVERT: A 291 GLN cc_start: 0.5660 (OUTLIER) cc_final: 0.5347 (mt0) REVERT: A 403 LYS cc_start: 0.6406 (pttt) cc_final: 0.5878 (tptp) REVERT: A 490 MET cc_start: 0.6461 (mpt) cc_final: 0.5543 (mpt) REVERT: A 530 LYS cc_start: 0.5902 (mtmt) cc_final: 0.5547 (mtmp) REVERT: A 534 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.7180 (p-80) outliers start: 11 outliers final: 6 residues processed: 52 average time/residue: 0.5392 time to fit residues: 29.2869 Evaluate side-chains 44 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.206418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.161395 restraints weight = 5455.851| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 2.44 r_work: 0.4248 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4757 Z= 0.131 Angle : 0.550 9.636 6432 Z= 0.294 Chirality : 0.040 0.128 719 Planarity : 0.004 0.034 837 Dihedral : 4.251 20.742 631 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.33 % Allowed : 20.74 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.34), residues: 590 helix: 1.18 (0.24), residues: 433 sheet: None (None), residues: 0 loop : -1.54 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 169 TYR 0.016 0.001 TYR A 164 PHE 0.030 0.002 PHE A 54 TRP 0.007 0.002 TRP A 181 HIS 0.007 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4741) covalent geometry : angle 0.54642 ( 6400) SS BOND : bond 0.00297 ( 16) SS BOND : angle 1.06423 ( 32) hydrogen bonds : bond 0.04041 ( 312) hydrogen bonds : angle 4.21409 ( 924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.171 Fit side-chains REVERT: A 43 LEU cc_start: 0.7119 (tp) cc_final: 0.6860 (tp) REVERT: A 124 CYS cc_start: 0.6520 (t) cc_final: 0.6020 (t) REVERT: A 228 LYS cc_start: 0.7749 (tttt) cc_final: 0.7090 (mppt) REVERT: A 403 LYS cc_start: 0.6511 (pttt) cc_final: 0.6069 (tptp) REVERT: A 448 MET cc_start: 0.6855 (mtm) cc_final: 0.6561 (mtp) REVERT: A 530 LYS cc_start: 0.5791 (mtmt) cc_final: 0.5440 (mtmp) REVERT: A 536 ASP cc_start: 0.5696 (p0) cc_final: 0.5401 (p0) outliers start: 12 outliers final: 6 residues processed: 47 average time/residue: 0.4341 time to fit residues: 21.5337 Evaluate side-chains 40 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 17 optimal weight: 0.0770 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.200101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.153620 restraints weight = 5415.798| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 2.43 r_work: 0.4157 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4757 Z= 0.200 Angle : 0.628 9.897 6432 Z= 0.335 Chirality : 0.044 0.139 719 Planarity : 0.004 0.040 837 Dihedral : 4.613 21.955 631 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.36 % Allowed : 22.67 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.34), residues: 590 helix: 0.74 (0.24), residues: 432 sheet: None (None), residues: 0 loop : -1.57 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 169 TYR 0.015 0.002 TYR A 185 PHE 0.024 0.002 PHE A 54 TRP 0.006 0.002 TRP A 181 HIS 0.007 0.002 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 4741) covalent geometry : angle 0.62119 ( 6400) SS BOND : bond 0.00484 ( 16) SS BOND : angle 1.43121 ( 32) hydrogen bonds : bond 0.04934 ( 312) hydrogen bonds : angle 4.52127 ( 924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7138 (tp) cc_final: 0.6877 (tp) REVERT: A 124 CYS cc_start: 0.6604 (t) cc_final: 0.6100 (t) REVERT: A 228 LYS cc_start: 0.7784 (tttt) cc_final: 0.7125 (mppt) REVERT: A 403 LYS cc_start: 0.6512 (pttt) cc_final: 0.6097 (tptp) REVERT: A 448 MET cc_start: 0.6963 (mtm) cc_final: 0.6692 (mtp) REVERT: A 490 MET cc_start: 0.6499 (mpt) cc_final: 0.5555 (mpt) REVERT: A 530 LYS cc_start: 0.5665 (mtmt) cc_final: 0.5308 (mtmp) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 0.4702 time to fit residues: 22.1985 Evaluate side-chains 42 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 462 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 41 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 0.0570 chunk 27 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.207190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.162466 restraints weight = 5453.442| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 2.42 r_work: 0.4258 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4757 Z= 0.125 Angle : 0.555 10.939 6432 Z= 0.296 Chirality : 0.039 0.127 719 Planarity : 0.004 0.034 837 Dihedral : 4.237 22.346 631 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.16 % Allowed : 22.67 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.35), residues: 590 helix: 1.23 (0.25), residues: 434 sheet: None (None), residues: 0 loop : -1.39 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 169 TYR 0.016 0.001 TYR A 164 PHE 0.026 0.002 PHE A 54 TRP 0.006 0.002 TRP A 181 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4741) covalent geometry : angle 0.55014 ( 6400) SS BOND : bond 0.00275 ( 16) SS BOND : angle 1.13927 ( 32) hydrogen bonds : bond 0.03880 ( 312) hydrogen bonds : angle 4.19055 ( 924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.177 Fit side-chains REVERT: A 43 LEU cc_start: 0.7100 (tp) cc_final: 0.6848 (tp) REVERT: A 124 CYS cc_start: 0.6516 (t) cc_final: 0.6046 (t) REVERT: A 228 LYS cc_start: 0.7726 (tttt) cc_final: 0.7083 (mppt) REVERT: A 254 GLU cc_start: 0.7067 (mp0) cc_final: 0.6686 (mp0) REVERT: A 403 LYS cc_start: 0.6416 (pttt) cc_final: 0.6068 (tptp) REVERT: A 448 MET cc_start: 0.6860 (mtm) cc_final: 0.6534 (mtp) REVERT: A 490 MET cc_start: 0.6479 (mpt) cc_final: 0.5550 (mpt) REVERT: A 530 LYS cc_start: 0.5734 (mtmt) cc_final: 0.5394 (mtmp) outliers start: 6 outliers final: 3 residues processed: 42 average time/residue: 0.5180 time to fit residues: 22.7988 Evaluate side-chains 39 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 462 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.207172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.162381 restraints weight = 5441.551| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 2.43 r_work: 0.4260 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4757 Z= 0.125 Angle : 0.557 10.924 6432 Z= 0.295 Chirality : 0.040 0.145 719 Planarity : 0.004 0.034 837 Dihedral : 4.136 21.925 631 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.97 % Allowed : 22.87 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.35), residues: 590 helix: 1.31 (0.24), residues: 434 sheet: None (None), residues: 0 loop : -1.35 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 169 TYR 0.008 0.001 TYR A 185 PHE 0.028 0.002 PHE A 54 TRP 0.007 0.002 TRP A 181 HIS 0.006 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4741) covalent geometry : angle 0.55141 ( 6400) SS BOND : bond 0.00276 ( 16) SS BOND : angle 1.22273 ( 32) hydrogen bonds : bond 0.03993 ( 312) hydrogen bonds : angle 4.12965 ( 924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2094.00 seconds wall clock time: 36 minutes 16.76 seconds (2176.76 seconds total)