Starting phenix.real_space_refine on Tue Aug 4 16:09:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rhf_53968/08_2026/9rhf_53968.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rhf_53968/08_2026/9rhf_53968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rhf_53968/08_2026/9rhf_53968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rhf_53968/08_2026/9rhf_53968.map" model { file = "/net/cci-nas-00/data/ceres_data/9rhf_53968/08_2026/9rhf_53968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rhf_53968/08_2026/9rhf_53968.cif" } resolution = 3.0 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= 0.002 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: 5 Type Number sf(0) Gaussians S 20 5.16 5 Na 1 4.78 5 C 3024 2.51 5 N 758 2.21 5 O 840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4643 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2917 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain: "B" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 816 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 1.21, per 1000 atoms: 0.26 Number of scatterers: 4643 At special positions: 0 Unit cell: (66.96, 80.352, 97.929, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 Na 1 11.00 O 840 8.00 N 758 7.00 C 3024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " 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: 0.38 Conformation dependent library (CDL) restraints added in 179.1 milliseconds 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1112 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 54.4% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 removed outlier: 3.605A pdb=" N SER A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 31 removed outlier: 4.260A pdb=" N GLY A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 59 through 66 Processing helix chain 'A' and resid 67 through 85 removed outlier: 3.847A pdb=" N PHE A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 89 removed outlier: 3.539A pdb=" N ALA A 89 " --> pdb=" O GLY A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 89' Processing helix chain 'A' and resid 90 through 117 removed outlier: 4.904A pdb=" N PHE A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix Proline residue: A 108 - end of helix removed outlier: 3.657A pdb=" N PHE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 removed outlier: 4.377A pdb=" N GLU A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 126 No H-bonds generated for 'chain 'A' and resid 125 through 126' Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.796A pdb=" N ALA A 131 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.735A pdb=" N LEU A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 149 through 175 Processing helix chain 'A' and resid 180 through 200 Processing helix chain 'A' and resid 204 through 222 removed outlier: 3.680A pdb=" N TYR A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.875A pdb=" N VAL A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 262 Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 282 through 285 Processing helix chain 'A' and resid 286 through 298 Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.519A pdb=" N ILE A 333 " --> pdb=" O MET A 329 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 354 through 382 removed outlier: 3.820A pdb=" N ILE A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.775A pdb=" N ASP B 31 " --> pdb=" O THR B 28 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'C' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.394A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.712A pdb=" N CYS B 96 " --> pdb=" O TRP B 108 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TRP B 108 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS B 98 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.346A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.556A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) 294 hydrogen bonds defined for protein. 813 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: 0.86 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 726 1.31 - 1.44: 1275 1.44 - 1.56: 2710 1.56 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 4744 Sorted by residual: bond pdb=" CG ASP A 163 " pdb=" OD1 ASP A 163 " ideal model delta sigma weight residual 1.249 1.184 0.065 1.90e-02 2.77e+03 1.17e+01 bond pdb=" N ASP B 104 " pdb=" CA ASP B 104 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 8.99e+00 bond pdb=" N ASN B 103 " pdb=" CA ASN B 103 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.65e+00 bond pdb=" C ASP B 90 " pdb=" N PRO B 91 " ideal model delta sigma weight residual 1.331 1.361 -0.030 1.28e-02 6.10e+03 5.39e+00 bond pdb=" N ASP C 1 " pdb=" CA ASP C 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 ... (remaining 4739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 6219 1.26 - 2.52: 176 2.52 - 3.78: 42 3.78 - 5.04: 12 5.04 - 6.29: 2 Bond angle restraints: 6451 Sorted by residual: angle pdb=" N ASN B 103 " pdb=" CA ASN B 103 " pdb=" C ASN B 103 " ideal model delta sigma weight residual 109.06 115.35 -6.29 1.70e+00 3.46e-01 1.37e+01 angle pdb=" CA ASP B 104 " pdb=" CB ASP B 104 " pdb=" CG ASP B 104 " ideal model delta sigma weight residual 112.60 115.96 -3.36 1.00e+00 1.00e+00 1.13e+01 angle pdb=" N PRO C 8 " pdb=" CA PRO C 8 " pdb=" CB PRO C 8 " ideal model delta sigma weight residual 102.92 104.78 -1.86 5.60e-01 3.19e+00 1.11e+01 angle pdb=" N ILE A 134 " pdb=" CA ILE A 134 " pdb=" C ILE A 134 " ideal model delta sigma weight residual 111.00 107.57 3.43 1.09e+00 8.42e-01 9.93e+00 angle pdb=" C GLY B 102 " pdb=" N ASN B 103 " pdb=" CA ASN B 103 " ideal model delta sigma weight residual 122.37 117.52 4.85 1.72e+00 3.38e-01 7.96e+00 ... (remaining 6446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 2521 17.21 - 34.41: 203 34.41 - 51.62: 42 51.62 - 68.82: 9 68.82 - 86.03: 3 Dihedral angle restraints: 2778 sinusoidal: 1034 harmonic: 1744 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.61 41.39 1 1.00e+01 1.00e-02 2.40e+01 dihedral pdb=" CA GLU B 99 " pdb=" C GLU B 99 " pdb=" N GLU B 100 " pdb=" CA GLU B 100 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 88 " pdb=" CB CYS C 88 " ideal model delta sinusoidal sigma weight residual 93.00 61.08 31.92 1 1.00e+01 1.00e-02 1.45e+01 ... (remaining 2775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 641 0.053 - 0.105: 106 0.105 - 0.158: 14 0.158 - 0.210: 0 0.210 - 0.263: 1 Chirality restraints: 762 Sorted by residual: chirality pdb=" CA ASP B 104 " pdb=" N ASP B 104 " pdb=" C ASP B 104 " pdb=" CB ASP B 104 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA VAL A 353 " pdb=" N VAL A 353 " pdb=" C VAL A 353 " pdb=" CB VAL A 353 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE A 237 " pdb=" N ILE A 237 " pdb=" C ILE A 237 " pdb=" CB ILE A 237 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 759 not shown) Planarity restraints: 794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 102 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C GLY B 102 " -0.039 2.00e-02 2.50e+03 pdb=" O GLY B 102 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN B 103 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 134 " -0.005 2.00e-02 2.50e+03 9.65e-03 9.31e-01 pdb=" C ILE A 134 " 0.017 2.00e-02 2.50e+03 pdb=" O ILE A 134 " -0.006 2.00e-02 2.50e+03 pdb=" N ALA A 135 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 128 " -0.016 5.00e-02 4.00e+02 2.36e-02 8.88e-01 pdb=" N PRO A 129 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.013 5.00e-02 4.00e+02 ... (remaining 791 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 214 2.73 - 3.27: 4852 3.27 - 3.81: 7757 3.81 - 4.36: 9470 4.36 - 4.90: 16516 Nonbonded interactions: 38809 Sorted by model distance: nonbonded pdb=" OD1 ASP A 164 " pdb="NA NA A 501 " model vdw 2.181 2.470 nonbonded pdb=" O THR A 132 " pdb="NA NA A 501 " model vdw 2.185 2.470 nonbonded pdb=" O ALA A 172 " pdb=" OG1 THR A 176 " model vdw 2.278 3.040 nonbonded pdb=" O ILE A 333 " pdb=" OG SER A 372 " model vdw 2.289 3.040 nonbonded pdb=" OG SER C 52 " pdb=" O GLY C 64 " model vdw 2.317 3.040 ... (remaining 38804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.890 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 4746 Z= 0.165 Angle : 0.557 6.294 6455 Z= 0.327 Chirality : 0.040 0.263 762 Planarity : 0.003 0.024 794 Dihedral : 13.435 86.029 1660 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.20 % Allowed : 11.38 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.30 (0.34), residues: 606 helix: 0.80 (0.30), residues: 292 sheet: 0.27 (0.48), residues: 118 loop : -0.59 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 92 TYR 0.009 0.001 TYR C 49 PHE 0.007 0.001 PHE C 98 TRP 0.006 0.001 TRP A 37 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 ( 4744) covalent geometry : angle 0.55734 / 0.33 ( 6451) SS BOND : bond 0.00139 / 0.07 ( 2) SS BOND : angle 0.33639 / 0.17 ( 4) hydrogen bonds : bond 0.20172 / 13.94 ( 279) hydrogen bonds : angle 8.30458 / 6.26 ( 813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.103 Fit side-chains REVERT: A 28 MET cc_start: 0.8678 (mmp) cc_final: 0.8263 (mmp) REVERT: A 119 ASP cc_start: 0.8204 (t0) cc_final: 0.7952 (t0) REVERT: C 78 LEU cc_start: 0.5541 (mt) cc_final: 0.4735 (tp) outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.4668 time to fit residues: 24.4026 Evaluate side-chains 49 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.0020 chunk 58 optimal weight: 3.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.187257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.103736 restraints weight = 5192.786| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.25 r_work: 0.2763 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4746 Z= 0.133 Angle : 0.595 8.846 6455 Z= 0.305 Chirality : 0.042 0.153 762 Planarity : 0.004 0.029 794 Dihedral : 4.765 21.793 654 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.03 % Allowed : 11.38 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.62 (0.34), residues: 606 helix: 1.07 (0.30), residues: 300 sheet: 0.31 (0.47), residues: 118 loop : -0.42 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 24 TYR 0.015 0.001 TYR C 49 PHE 0.011 0.001 PHE C 96 TRP 0.010 0.001 TRP C 35 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 4744) covalent geometry : angle 0.59470 / 0.30 ( 6451) SS BOND : bond 0.00742 / 0.35 ( 2) SS BOND : angle 1.10832 / 0.46 ( 4) hydrogen bonds : bond 0.03862 / 2.72 ( 279) hydrogen bonds : angle 5.64329 / 4.23 ( 813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.182 Fit side-chains REVERT: A 28 MET cc_start: 0.8482 (mmp) cc_final: 0.8101 (mmp) REVERT: A 93 GLN cc_start: 0.8194 (mt0) cc_final: 0.7733 (mt0) REVERT: B 34 MET cc_start: 0.8215 (mtp) cc_final: 0.7993 (mtm) REVERT: C 78 LEU cc_start: 0.5334 (mt) cc_final: 0.4613 (tp) outliers start: 10 outliers final: 1 residues processed: 59 average time/residue: 0.4070 time to fit residues: 25.0143 Evaluate side-chains 48 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 42 optimal weight: 0.0170 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.187963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.104635 restraints weight = 5111.799| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.22 r_work: 0.2792 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4746 Z= 0.116 Angle : 0.538 8.466 6455 Z= 0.275 Chirality : 0.041 0.161 762 Planarity : 0.004 0.038 794 Dihedral : 4.537 20.354 652 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.44 % Allowed : 11.38 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.89 (0.34), residues: 606 helix: 1.29 (0.31), residues: 300 sheet: 0.43 (0.45), residues: 117 loop : -0.29 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 92 TYR 0.012 0.001 TYR C 49 PHE 0.008 0.001 PHE C 96 TRP 0.008 0.001 TRP C 35 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 4744) covalent geometry : angle 0.53765 / 0.28 ( 6451) SS BOND : bond 0.00421 / 0.20 ( 2) SS BOND : angle 0.52057 / 0.23 ( 4) hydrogen bonds : bond 0.03384 / 2.38 ( 279) hydrogen bonds : angle 5.15965 / 3.86 ( 813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.180 Fit side-chains REVERT: A 28 MET cc_start: 0.8447 (mmp) cc_final: 0.8051 (mmp) REVERT: A 47 GLN cc_start: 0.8865 (mt0) cc_final: 0.8633 (mt0) REVERT: A 93 GLN cc_start: 0.8267 (mt0) cc_final: 0.7972 (mt0) REVERT: A 157 MET cc_start: 0.8355 (mtm) cc_final: 0.8153 (mtp) REVERT: A 241 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7934 (mm-30) REVERT: B 48 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6653 (OUTLIER) REVERT: B 105 PHE cc_start: 0.6950 (m-80) cc_final: 0.6730 (m-80) REVERT: C 78 LEU cc_start: 0.5358 (mt) cc_final: 0.4598 (tp) outliers start: 12 outliers final: 4 residues processed: 57 average time/residue: 0.4032 time to fit residues: 24.0279 Evaluate side-chains 52 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 56 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 40.0000 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.186335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.108420 restraints weight = 5101.562| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.55 r_work: 0.2870 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4746 Z= 0.141 Angle : 0.559 8.403 6455 Z= 0.281 Chirality : 0.042 0.167 762 Planarity : 0.004 0.040 794 Dihedral : 4.487 19.917 652 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.98 % Favored : 97.85 % Rotamer: Outliers : 3.46 % Allowed : 11.59 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.92 (0.34), residues: 606 helix: 1.28 (0.30), residues: 300 sheet: 0.55 (0.46), residues: 117 loop : -0.29 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 92 TYR 0.012 0.001 TYR C 49 PHE 0.008 0.001 PHE C 98 TRP 0.008 0.001 TRP A 37 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 4744) covalent geometry : angle 0.55873 / 0.28 ( 6451) SS BOND : bond 0.00426 / 0.20 ( 2) SS BOND : angle 0.64733 / 0.29 ( 4) hydrogen bonds : bond 0.03356 / 2.35 ( 279) hydrogen bonds : angle 5.06480 / 3.80 ( 813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.182 Fit side-chains REVERT: A 28 MET cc_start: 0.8626 (mmp) cc_final: 0.8251 (mmp) REVERT: A 47 GLN cc_start: 0.8904 (mt0) cc_final: 0.8680 (mt0) REVERT: A 93 GLN cc_start: 0.8380 (mt0) cc_final: 0.7969 (mt0) REVERT: A 153 LYS cc_start: 0.7618 (mttt) cc_final: 0.7383 (ttmm) REVERT: A 183 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.8336 (p) REVERT: A 241 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8035 (mm-30) REVERT: B 34 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8164 (mmt) REVERT: B 48 ILE cc_start: 0.6966 (OUTLIER) cc_final: 0.6519 (OUTLIER) REVERT: B 51 ILE cc_start: 0.6848 (OUTLIER) cc_final: 0.6605 (mp) REVERT: C 78 LEU cc_start: 0.5432 (mt) cc_final: 0.4643 (tp) outliers start: 17 outliers final: 5 residues processed: 62 average time/residue: 0.5883 time to fit residues: 37.9406 Evaluate side-chains 60 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 89 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.187350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.109324 restraints weight = 5076.936| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.76 r_work: 0.2792 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4746 Z= 0.123 Angle : 0.533 7.994 6455 Z= 0.269 Chirality : 0.041 0.158 762 Planarity : 0.004 0.041 794 Dihedral : 4.415 19.585 652 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.98 % Favored : 97.85 % Rotamer: Outliers : 3.86 % Allowed : 12.20 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.95 (0.34), residues: 606 helix: 1.34 (0.30), residues: 300 sheet: 0.59 (0.46), residues: 117 loop : -0.36 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 92 TYR 0.011 0.001 TYR C 49 PHE 0.009 0.001 PHE B 105 TRP 0.007 0.001 TRP A 37 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 4744) covalent geometry : angle 0.53257 / 0.27 ( 6451) SS BOND : bond 0.00348 / 0.17 ( 2) SS BOND : angle 0.44630 / 0.22 ( 4) hydrogen bonds : bond 0.03143 / 2.20 ( 279) hydrogen bonds : angle 4.91839 / 3.69 ( 813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.178 Fit side-chains REVERT: A 28 MET cc_start: 0.8468 (mmp) cc_final: 0.8117 (mmp) REVERT: A 47 GLN cc_start: 0.8851 (mt0) cc_final: 0.8600 (mt0) REVERT: A 93 GLN cc_start: 0.8334 (mt0) cc_final: 0.8013 (mt0) REVERT: A 183 SER cc_start: 0.8446 (OUTLIER) cc_final: 0.8226 (p) REVERT: A 241 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8052 (mm-30) REVERT: B 34 MET cc_start: 0.8436 (mtp) cc_final: 0.8156 (mmt) REVERT: B 48 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6452 (OUTLIER) outliers start: 19 outliers final: 9 residues processed: 62 average time/residue: 0.5632 time to fit residues: 36.4014 Evaluate side-chains 59 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 89 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.186851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103667 restraints weight = 5179.333| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.19 r_work: 0.2770 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4746 Z= 0.129 Angle : 0.540 7.751 6455 Z= 0.269 Chirality : 0.041 0.165 762 Planarity : 0.004 0.045 794 Dihedral : 4.370 19.571 652 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.48 % Favored : 97.36 % Rotamer: Outliers : 4.07 % Allowed : 12.20 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.02 (0.34), residues: 606 helix: 1.34 (0.30), residues: 305 sheet: 0.70 (0.46), residues: 117 loop : -0.35 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 92 TYR 0.011 0.001 TYR C 49 PHE 0.009 0.001 PHE B 105 TRP 0.007 0.001 TRP A 37 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 4744) covalent geometry : angle 0.53976 / 0.27 ( 6451) SS BOND : bond 0.00404 / 0.19 ( 2) SS BOND : angle 0.61457 / 0.28 ( 4) hydrogen bonds : bond 0.03139 / 2.19 ( 279) hydrogen bonds : angle 4.86750 / 3.67 ( 813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.177 Fit side-chains REVERT: A 28 MET cc_start: 0.8431 (mmp) cc_final: 0.8081 (mmp) REVERT: A 47 GLN cc_start: 0.8782 (mt0) cc_final: 0.8528 (mt0) REVERT: A 93 GLN cc_start: 0.8329 (mt0) cc_final: 0.8007 (mt0) REVERT: A 153 LYS cc_start: 0.7373 (mttt) cc_final: 0.7154 (ttmm) REVERT: A 183 SER cc_start: 0.8384 (OUTLIER) cc_final: 0.8154 (p) REVERT: A 241 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8063 (mm-30) REVERT: B 34 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8157 (mmt) REVERT: B 48 ILE cc_start: 0.6866 (OUTLIER) cc_final: 0.6468 (OUTLIER) outliers start: 20 outliers final: 11 residues processed: 64 average time/residue: 0.4827 time to fit residues: 32.2425 Evaluate side-chains 67 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 89 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 46 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.186219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.102727 restraints weight = 5138.312| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.21 r_work: 0.2755 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4746 Z= 0.139 Angle : 0.544 6.140 6455 Z= 0.273 Chirality : 0.042 0.162 762 Planarity : 0.004 0.044 794 Dihedral : 4.409 19.435 652 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.82 % Favored : 98.02 % Rotamer: Outliers : 3.46 % Allowed : 13.01 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.09 (0.34), residues: 606 helix: 1.36 (0.30), residues: 304 sheet: 0.90 (0.47), residues: 115 loop : -0.33 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 92 TYR 0.011 0.001 TYR C 49 PHE 0.008 0.001 PHE B 105 TRP 0.007 0.001 TRP A 37 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 4744) covalent geometry : angle 0.54357 / 0.27 ( 6451) SS BOND : bond 0.00369 / 0.18 ( 2) SS BOND : angle 0.54187 / 0.26 ( 4) hydrogen bonds : bond 0.03197 / 2.24 ( 279) hydrogen bonds : angle 4.86740 / 3.68 ( 813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.172 Fit side-chains REVERT: A 28 MET cc_start: 0.8412 (mmp) cc_final: 0.8081 (mmp) REVERT: A 47 GLN cc_start: 0.8779 (mt0) cc_final: 0.8526 (mt0) REVERT: A 153 LYS cc_start: 0.7414 (mttt) cc_final: 0.7196 (ttmm) REVERT: A 183 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.8150 (p) REVERT: A 241 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8046 (mm-30) REVERT: B 34 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8144 (mmt) REVERT: B 48 ILE cc_start: 0.6815 (OUTLIER) cc_final: 0.6423 (OUTLIER) outliers start: 17 outliers final: 11 residues processed: 60 average time/residue: 0.5478 time to fit residues: 34.2911 Evaluate side-chains 63 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 89 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.188362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.110929 restraints weight = 5198.194| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.60 r_work: 0.2805 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4746 Z= 0.106 Angle : 0.519 7.294 6455 Z= 0.261 Chirality : 0.040 0.161 762 Planarity : 0.004 0.045 794 Dihedral : 4.233 19.459 652 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.15 % Favored : 97.69 % Rotamer: Outliers : 3.25 % Allowed : 14.23 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.30 (0.34), residues: 606 helix: 1.62 (0.31), residues: 298 sheet: 0.92 (0.47), residues: 115 loop : -0.28 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 92 TYR 0.011 0.001 TYR C 49 PHE 0.013 0.001 PHE B 105 TRP 0.006 0.001 TRP A 37 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 4744) covalent geometry : angle 0.51884 / 0.26 ( 6451) SS BOND : bond 0.00374 / 0.18 ( 2) SS BOND : angle 0.46079 / 0.22 ( 4) hydrogen bonds : bond 0.02868 / 2.02 ( 279) hydrogen bonds : angle 4.67386 / 3.53 ( 813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.141 Fit side-chains REVERT: A 28 MET cc_start: 0.8427 (mmp) cc_final: 0.8099 (mmp) REVERT: A 47 GLN cc_start: 0.8724 (mt0) cc_final: 0.8484 (mt0) REVERT: A 241 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8073 (mm-30) REVERT: B 34 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8209 (mmt) outliers start: 16 outliers final: 9 residues processed: 61 average time/residue: 0.4788 time to fit residues: 30.4360 Evaluate side-chains 60 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 89 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 12 optimal weight: 0.0870 chunk 57 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 25 optimal weight: 0.4980 chunk 46 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.187399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.110464 restraints weight = 5066.849| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.42 r_work: 0.2911 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4746 Z= 0.122 Angle : 0.534 7.367 6455 Z= 0.268 Chirality : 0.040 0.160 762 Planarity : 0.004 0.047 794 Dihedral : 4.258 19.294 652 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.82 % Favored : 98.02 % Rotamer: Outliers : 3.05 % Allowed : 14.23 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.27 (0.34), residues: 606 helix: 1.60 (0.31), residues: 298 sheet: 0.91 (0.47), residues: 117 loop : -0.32 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 92 TYR 0.011 0.001 TYR C 49 PHE 0.012 0.001 PHE B 105 TRP 0.007 0.001 TRP A 37 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 4744) covalent geometry : angle 0.53363 / 0.27 ( 6451) SS BOND : bond 0.00355 / 0.17 ( 2) SS BOND : angle 0.48719 / 0.24 ( 4) hydrogen bonds : bond 0.02989 / 2.10 ( 279) hydrogen bonds : angle 4.75048 / 3.60 ( 813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.177 Fit side-chains REVERT: A 28 MET cc_start: 0.8608 (mmp) cc_final: 0.8274 (mmp) REVERT: A 47 GLN cc_start: 0.8742 (mt0) cc_final: 0.8529 (mt0) REVERT: A 241 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8068 (mm-30) REVERT: B 34 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8292 (mmt) outliers start: 15 outliers final: 9 residues processed: 59 average time/residue: 0.4888 time to fit residues: 30.0915 Evaluate side-chains 62 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 89 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 51 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 8 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.187419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.110265 restraints weight = 5136.778| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.54 r_work: 0.2756 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4746 Z= 0.124 Angle : 0.535 6.615 6455 Z= 0.269 Chirality : 0.041 0.160 762 Planarity : 0.004 0.047 794 Dihedral : 4.301 19.205 652 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.15 % Favored : 97.69 % Rotamer: Outliers : 2.64 % Allowed : 14.43 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.35 (0.34), residues: 606 helix: 1.59 (0.30), residues: 298 sheet: 1.14 (0.48), residues: 115 loop : -0.27 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 92 TYR 0.010 0.001 TYR C 49 PHE 0.014 0.001 PHE B 105 TRP 0.006 0.001 TRP A 37 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 ( 4744) covalent geometry : angle 0.53487 / 0.27 ( 6451) SS BOND : bond 0.00356 / 0.17 ( 2) SS BOND : angle 0.51589 / 0.26 ( 4) hydrogen bonds : bond 0.03025 / 2.13 ( 279) hydrogen bonds : angle 4.75111 / 3.60 ( 813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.196 Fit side-chains REVERT: A 28 MET cc_start: 0.8425 (mmp) cc_final: 0.8112 (mmp) REVERT: A 47 GLN cc_start: 0.8745 (mt0) cc_final: 0.8503 (mt0) REVERT: A 153 LYS cc_start: 0.7364 (mttt) cc_final: 0.7128 (ttmm) REVERT: A 241 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8044 (mm-30) REVERT: B 34 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8176 (mmt) REVERT: B 48 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6846 (tt) outliers start: 13 outliers final: 9 residues processed: 59 average time/residue: 0.5390 time to fit residues: 33.1636 Evaluate side-chains 62 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 89 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 47 optimal weight: 5.9990 chunk 9 optimal weight: 0.1980 chunk 45 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.188079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.106010 restraints weight = 5149.704| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.22 r_work: 0.2797 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4746 Z= 0.113 Angle : 0.521 7.183 6455 Z= 0.262 Chirality : 0.040 0.157 762 Planarity : 0.004 0.047 794 Dihedral : 4.213 19.211 652 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.98 % Favored : 97.85 % Rotamer: Outliers : 2.64 % Allowed : 14.63 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.37 (0.34), residues: 606 helix: 1.63 (0.31), residues: 298 sheet: 1.13 (0.48), residues: 115 loop : -0.29 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 92 TYR 0.010 0.001 TYR C 49 PHE 0.015 0.001 PHE B 105 TRP 0.006 0.001 TRP A 37 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 4744) covalent geometry : angle 0.52060 / 0.26 ( 6451) SS BOND : bond 0.00346 / 0.17 ( 2) SS BOND : angle 0.44304 / 0.22 ( 4) hydrogen bonds : bond 0.02908 / 2.05 ( 279) hydrogen bonds : angle 4.70047 / 3.57 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1746.08 seconds wall clock time: 30 minutes 30.37 seconds (1830.37 seconds total)