Starting phenix.real_space_refine on Wed Aug 5 01:12:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w43_65617/08_2026/9w43_65617.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w43_65617/08_2026/9w43_65617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w43_65617/08_2026/9w43_65617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w43_65617/08_2026/9w43_65617.map" model { file = "/net/cci-nas-00/data/ceres_data/9w43_65617/08_2026/9w43_65617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w43_65617/08_2026/9w43_65617.cif" } resolution = 2.96 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= 0.043 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 16 5.16 5 C 2462 2.51 5 N 656 2.21 5 O 766 1.98 5 H 3793 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s 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: 7693 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3180 Classifications: {'peptide': 213} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain breaks: 1 Chain: "B" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3218 Classifications: {'peptide': 211} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain: "C" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1295 Classifications: {'peptide': 83} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain breaks: 4 Time building chain proxies: 1.21, per 1000 atoms: 0.16 Number of scatterers: 7693 At special positions: 0 Unit cell: (55.692, 68.796, 104.832, 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 16 16.00 O 766 8.00 N 656 7.00 C 2462 6.00 H 3793 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 123 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 323.7 milliseconds 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 942 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 13 sheets defined 7.5% alpha, 50.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.878A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.757A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.567A pdb=" N VAL B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'C' and resid 114 through 118 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.798A pdb=" N ILE A 34 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.777A pdb=" N TYR A 108 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 130 removed outlier: 6.051A pdb=" N TYR A 182 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 126 through 130 removed outlier: 6.051A pdb=" N TYR A 182 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 157 through 160 removed outlier: 4.342A pdb=" N TYR A 200 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.836A pdb=" N ASP B 70 " --> pdb=" O TYR B 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.370A pdb=" N LEU B 11 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.370A pdb=" N LEU B 11 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 96 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 113 through 117 removed outlier: 5.866A pdb=" N TYR B 172 " --> pdb=" O ASN B 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 152 through 154 removed outlier: 4.690A pdb=" N TRP B 147 " --> pdb=" O GLN B 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 36 through 37 Processing sheet with id=AB4, first strand: chain 'C' and resid 41 through 45 removed outlier: 6.626A pdb=" N LEU C 42 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR C 145 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 44 " --> pdb=" O THR C 145 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR C 120 " --> pdb=" O MET C 70 " (cutoff:3.500A) 180 hydrogen bonds defined for protein. 438 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 3793 1.02 - 1.22: 5 1.22 - 1.42: 1696 1.42 - 1.62: 2266 1.62 - 1.82: 22 Bond restraints: 7782 Sorted by residual: bond pdb=" ND2 ASN B 31 " pdb="HD22 ASN B 31 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN B 32 " pdb="HD21 ASN B 32 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN C 116 " pdb="HD22 ASN C 116 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN C 116 " pdb="HD21 ASN C 116 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN B 31 " pdb="HD21 ASN B 31 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.55e+01 ... (remaining 7777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 13266 1.16 - 2.33: 658 2.33 - 3.49: 52 3.49 - 4.66: 22 4.66 - 5.82: 6 Bond angle restraints: 14004 Sorted by residual: angle pdb=" N ASP C 117 " pdb=" CA ASP C 117 " pdb=" C ASP C 117 " ideal model delta sigma weight residual 112.88 107.71 5.17 1.29e+00 6.01e-01 1.60e+01 angle pdb=" C SER B 94 " pdb=" CA SER B 94 " pdb=" CB SER B 94 " ideal model delta sigma weight residual 116.63 112.04 4.59 1.16e+00 7.43e-01 1.57e+01 angle pdb=" N ASP C 77 " pdb=" CA ASP C 77 " pdb=" C ASP C 77 " ideal model delta sigma weight residual 113.61 107.79 5.82 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C THR B 30 " pdb=" CA THR B 30 " pdb=" CB THR B 30 " ideal model delta sigma weight residual 117.23 112.37 4.86 1.36e+00 5.41e-01 1.28e+01 angle pdb=" N VAL B 33 " pdb=" CA VAL B 33 " pdb=" C VAL B 33 " ideal model delta sigma weight residual 108.35 112.86 -4.51 1.32e+00 5.74e-01 1.17e+01 ... (remaining 13999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3407 17.80 - 35.61: 239 35.61 - 53.41: 70 53.41 - 71.21: 16 71.21 - 89.02: 10 Dihedral angle restraints: 3742 sinusoidal: 2006 harmonic: 1736 Sorted by residual: dihedral pdb=" CA PHE C 37 " pdb=" C PHE C 37 " pdb=" N SER C 38 " pdb=" CA SER C 38 " ideal model delta harmonic sigma weight residual -180.00 -152.80 -27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CB CYS A 146 " pdb=" SG CYS A 146 " pdb=" SG CYS A 202 " pdb=" CB CYS A 202 " ideal model delta sinusoidal sigma weight residual 93.00 128.01 -35.01 1 1.00e+01 1.00e-02 1.74e+01 dihedral pdb=" CA ASN B 136 " pdb=" C ASN B 136 " pdb=" N ASN B 137 " pdb=" CA ASN B 137 " ideal model delta harmonic sigma weight residual 180.00 163.38 16.62 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 3739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 356 0.032 - 0.064: 167 0.064 - 0.096: 38 0.096 - 0.128: 46 0.128 - 0.160: 5 Chirality restraints: 612 Sorted by residual: chirality pdb=" CA ILE A 37 " pdb=" N ILE A 37 " pdb=" C ILE A 37 " pdb=" CB ILE A 37 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA THR B 30 " pdb=" N THR B 30 " pdb=" C THR B 30 " pdb=" CB THR B 30 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA VAL A 148 " pdb=" N VAL A 148 " pdb=" C VAL A 148 " pdb=" CB VAL A 148 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 609 not shown) Planarity restraints: 1161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 116 " -0.317 2.00e-02 2.50e+03 3.81e-01 2.18e+03 pdb=" CG ASN C 116 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 116 " 0.305 2.00e-02 2.50e+03 pdb=" ND2 ASN C 116 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN C 116 " 0.574 2.00e-02 2.50e+03 pdb="HD22 ASN C 116 " -0.591 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 31 " -0.307 2.00e-02 2.50e+03 3.44e-01 1.77e+03 pdb=" CG ASN B 31 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 31 " 0.291 2.00e-02 2.50e+03 pdb=" ND2 ASN B 31 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN B 31 " -0.524 2.00e-02 2.50e+03 pdb="HD22 ASN B 31 " 0.504 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 90 " 0.188 2.00e-02 2.50e+03 2.17e-01 7.08e+02 pdb=" CD GLN B 90 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN B 90 " -0.181 2.00e-02 2.50e+03 pdb=" NE2 GLN B 90 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 90 " 0.331 2.00e-02 2.50e+03 pdb="HE22 GLN B 90 " -0.324 2.00e-02 2.50e+03 ... (remaining 1158 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.24: 932 2.24 - 2.83: 16987 2.83 - 3.42: 19366 3.42 - 4.01: 28806 4.01 - 4.60: 42607 Nonbonded interactions: 108698 Sorted by model distance: nonbonded pdb=" H MET A 106 " pdb=" OH TYR B 36 " model vdw 1.644 2.450 nonbonded pdb=" O ASP B 82 " pdb=" HH TYR B 86 " model vdw 1.672 2.450 nonbonded pdb=" H GLY A 15 " pdb=" O LEU A 86 " model vdw 1.680 2.450 nonbonded pdb="HE22 GLN A 6 " pdb=" O TYR A 94 " model vdw 1.712 2.450 nonbonded pdb=" HH TYR A 59 " pdb=" OD2 ASP C 105 " model vdw 1.716 2.450 ... (remaining 108693 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.440 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:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 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 : 0.004 0.034 3994 Z= 0.207 Angle : 0.635 5.825 5435 Z= 0.368 Chirality : 0.047 0.160 612 Planarity : 0.004 0.043 690 Dihedral : 12.961 89.016 1422 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: 0.55 (0.40), residues: 491 helix: -0.60 (1.34), residues: 15 sheet: 0.70 (0.32), residues: 268 loop : 0.13 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 50 TYR 0.014 0.001 TYR C 121 PHE 0.016 0.001 PHE C 37 TRP 0.006 0.001 TRP B 95 HIS 0.002 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.21 ( 3989) covalent geometry : angle 0.63369 / 0.37 ( 5425) SS BOND : bond 0.00373 / 0.20 ( 5) SS BOND : angle 1.06011 / 0.68 ( 10) hydrogen bonds : bond 0.11515 / 7.67 ( 156) hydrogen bonds : angle 6.22464 / 4.29 ( 438) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.6784 (t0) cc_final: 0.6565 (t0) REVERT: B 102 LYS cc_start: 0.7584 (ttpp) cc_final: 0.7355 (tttt) REVERT: B 144 LYS cc_start: 0.6797 (tppt) cc_final: 0.6339 (tppt) REVERT: B 146 GLN cc_start: 0.7136 (mt0) cc_final: 0.6243 (mt0) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.8753 time to fit residues: 72.2739 Evaluate side-chains 62 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 63.4284 > 50:) chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.137927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.123180 restraints weight = 14164.890| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.74 r_work: 0.3295 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3994 Z= 0.144 Angle : 0.530 6.448 5435 Z= 0.273 Chirality : 0.045 0.146 612 Planarity : 0.004 0.035 690 Dihedral : 4.354 22.859 544 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.83 % Allowed : 7.78 % Favored : 90.39 % 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: 0.67 (0.41), residues: 491 helix: -0.65 (1.34), residues: 15 sheet: 0.83 (0.33), residues: 260 loop : 0.17 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 115 TYR 0.009 0.001 TYR B 139 PHE 0.010 0.001 PHE C 37 TRP 0.007 0.001 TRP B 95 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 3989) covalent geometry : angle 0.52867 / 0.27 ( 5425) SS BOND : bond 0.00288 / 0.16 ( 5) SS BOND : angle 0.98238 / 0.63 ( 10) hydrogen bonds : bond 0.03340 / 2.21 ( 156) hydrogen bonds : angle 5.42132 / 3.82 ( 438) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 144 LYS cc_start: 0.7687 (tppt) cc_final: 0.7479 (tppt) REVERT: B 146 GLN cc_start: 0.7866 (mt0) cc_final: 0.7200 (mt0) outliers start: 8 outliers final: 7 residues processed: 64 average time/residue: 0.9307 time to fit residues: 62.1687 Evaluate side-chains 64 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain C residue 108 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 ASN C 66 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.137964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.122891 restraints weight = 14029.198| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.75 r_work: 0.3298 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3994 Z= 0.141 Angle : 0.516 5.892 5435 Z= 0.264 Chirality : 0.045 0.145 612 Planarity : 0.004 0.033 690 Dihedral : 4.327 23.055 544 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.29 % Allowed : 8.92 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.41), residues: 491 helix: -0.78 (1.32), residues: 15 sheet: 0.88 (0.34), residues: 259 loop : 0.16 (0.48), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 147 TYR 0.008 0.001 TYR B 139 PHE 0.009 0.001 PHE C 37 TRP 0.004 0.001 TRP A 109 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 3989) covalent geometry : angle 0.51455 / 0.26 ( 5425) SS BOND : bond 0.00281 / 0.15 ( 5) SS BOND : angle 1.00002 / 0.72 ( 10) hydrogen bonds : bond 0.03003 / 2.00 ( 156) hydrogen bonds : angle 5.23027 / 3.71 ( 438) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: B 141 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7021 (ttm-80) REVERT: B 146 GLN cc_start: 0.7893 (mt0) cc_final: 0.7141 (mt0) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.8210 time to fit residues: 58.5483 Evaluate side-chains 62 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain C residue 108 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 ASN C 66 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.136087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.121321 restraints weight = 14276.269| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.72 r_work: 0.3239 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3994 Z= 0.165 Angle : 0.532 5.653 5435 Z= 0.272 Chirality : 0.046 0.146 612 Planarity : 0.004 0.033 690 Dihedral : 4.469 24.230 544 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.52 % Allowed : 10.98 % Favored : 86.50 % 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: 0.57 (0.40), residues: 491 helix: -0.94 (1.28), residues: 15 sheet: 0.80 (0.33), residues: 259 loop : 0.07 (0.47), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 147 TYR 0.008 0.001 TYR A 95 PHE 0.008 0.001 PHE C 37 TRP 0.004 0.001 TRP A 109 HIS 0.003 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 ( 3989) covalent geometry : angle 0.53069 / 0.27 ( 5425) SS BOND : bond 0.00307 / 0.16 ( 5) SS BOND : angle 1.01458 / 0.74 ( 10) hydrogen bonds : bond 0.02912 / 1.96 ( 156) hydrogen bonds : angle 5.23369 / 3.73 ( 438) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8056 (tp) REVERT: B 141 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7004 (ttm-80) REVERT: B 146 GLN cc_start: 0.7988 (mt0) cc_final: 0.7197 (mt0) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.7146 time to fit residues: 48.0136 Evaluate side-chains 64 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 108 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.136754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.121998 restraints weight = 14189.047| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.73 r_work: 0.3244 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3994 Z= 0.129 Angle : 0.507 5.003 5435 Z= 0.259 Chirality : 0.045 0.144 612 Planarity : 0.003 0.032 690 Dihedral : 4.344 23.099 544 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.52 % Allowed : 12.13 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.40), residues: 491 helix: -0.83 (1.30), residues: 15 sheet: 0.79 (0.33), residues: 259 loop : 0.13 (0.47), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 147 TYR 0.008 0.001 TYR B 139 PHE 0.009 0.001 PHE C 37 TRP 0.004 0.001 TRP A 160 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 3989) covalent geometry : angle 0.50598 / 0.26 ( 5425) SS BOND : bond 0.00328 / 0.17 ( 5) SS BOND : angle 0.92264 / 0.70 ( 10) hydrogen bonds : bond 0.02728 / 1.84 ( 156) hydrogen bonds : angle 5.07975 / 3.63 ( 438) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8003 (tp) REVERT: B 146 GLN cc_start: 0.7966 (mt0) cc_final: 0.7114 (mt0) outliers start: 11 outliers final: 7 residues processed: 62 average time/residue: 0.7883 time to fit residues: 51.1657 Evaluate side-chains 61 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 108 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 12 optimal weight: 0.0770 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.137502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122847 restraints weight = 14272.538| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.73 r_work: 0.3262 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3994 Z= 0.117 Angle : 0.498 4.934 5435 Z= 0.254 Chirality : 0.045 0.147 612 Planarity : 0.003 0.032 690 Dihedral : 4.269 22.307 544 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.06 % Allowed : 12.13 % Favored : 85.81 % 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: 0.62 (0.41), residues: 491 helix: -0.74 (1.32), residues: 15 sheet: 0.78 (0.33), residues: 259 loop : 0.16 (0.47), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 139 TYR 0.008 0.001 TYR B 139 PHE 0.008 0.001 PHE C 37 TRP 0.005 0.001 TRP A 160 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 3989) covalent geometry : angle 0.49738 / 0.25 ( 5425) SS BOND : bond 0.00236 / 0.12 ( 5) SS BOND : angle 0.81338 / 0.59 ( 10) hydrogen bonds : bond 0.02662 / 1.82 ( 156) hydrogen bonds : angle 5.03969 / 3.61 ( 438) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8021 (tp) REVERT: B 93 SER cc_start: 0.8321 (t) cc_final: 0.7856 (p) REVERT: B 146 GLN cc_start: 0.7946 (mt0) cc_final: 0.7060 (mt0) outliers start: 9 outliers final: 7 residues processed: 62 average time/residue: 0.7646 time to fit residues: 49.7328 Evaluate side-chains 62 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 108 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.136898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.122151 restraints weight = 14121.457| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.74 r_work: 0.3254 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3994 Z= 0.141 Angle : 0.510 5.038 5435 Z= 0.260 Chirality : 0.045 0.146 612 Planarity : 0.004 0.032 690 Dihedral : 4.332 23.342 544 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.52 % Allowed : 12.36 % Favored : 85.13 % 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: 0.54 (0.40), residues: 491 helix: -0.92 (1.29), residues: 15 sheet: 0.73 (0.33), residues: 259 loop : 0.13 (0.47), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 141 TYR 0.008 0.001 TYR A 95 PHE 0.008 0.001 PHE C 37 TRP 0.004 0.001 TRP A 109 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 3989) covalent geometry : angle 0.50855 / 0.26 ( 5425) SS BOND : bond 0.00267 / 0.14 ( 5) SS BOND : angle 1.04729 / 0.73 ( 10) hydrogen bonds : bond 0.02748 / 1.88 ( 156) hydrogen bonds : angle 5.07297 / 3.63 ( 438) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8055 (tp) REVERT: B 93 SER cc_start: 0.8310 (t) cc_final: 0.7852 (p) REVERT: B 146 GLN cc_start: 0.7968 (mt0) cc_final: 0.7084 (mt0) outliers start: 11 outliers final: 9 residues processed: 65 average time/residue: 0.8150 time to fit residues: 55.4798 Evaluate side-chains 65 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 108 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.137445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.122761 restraints weight = 14303.890| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.73 r_work: 0.3251 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3994 Z= 0.125 Angle : 0.500 4.998 5435 Z= 0.256 Chirality : 0.045 0.144 612 Planarity : 0.003 0.032 690 Dihedral : 4.273 22.722 544 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.75 % Allowed : 12.13 % Favored : 85.13 % 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: 0.60 (0.41), residues: 491 helix: -0.81 (1.31), residues: 15 sheet: 0.75 (0.33), residues: 259 loop : 0.19 (0.47), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 139 TYR 0.009 0.001 TYR C 121 PHE 0.008 0.001 PHE C 37 TRP 0.005 0.001 TRP A 160 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 ( 3989) covalent geometry : angle 0.49938 / 0.26 ( 5425) SS BOND : bond 0.00203 / 0.11 ( 5) SS BOND : angle 0.92122 / 0.69 ( 10) hydrogen bonds : bond 0.02651 / 1.81 ( 156) hydrogen bonds : angle 5.02362 / 3.59 ( 438) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8010 (tp) REVERT: B 93 SER cc_start: 0.8316 (t) cc_final: 0.7865 (p) REVERT: B 104 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8079 (pt0) REVERT: B 141 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7187 (ttm-80) REVERT: B 146 GLN cc_start: 0.7967 (mt0) cc_final: 0.7065 (mt0) outliers start: 12 outliers final: 8 residues processed: 63 average time/residue: 0.7490 time to fit residues: 49.3783 Evaluate side-chains 66 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 108 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 0 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.138005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.123372 restraints weight = 14280.467| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.71 r_work: 0.3273 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3994 Z= 0.107 Angle : 0.492 4.997 5435 Z= 0.251 Chirality : 0.045 0.143 612 Planarity : 0.003 0.031 690 Dihedral : 4.197 21.855 544 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.29 % Allowed : 12.81 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.41), residues: 491 helix: -0.66 (1.34), residues: 15 sheet: 0.79 (0.33), residues: 259 loop : 0.23 (0.47), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 147 TYR 0.009 0.001 TYR C 121 PHE 0.008 0.001 PHE C 37 TRP 0.006 0.001 TRP A 160 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 3989) covalent geometry : angle 0.49082 / 0.25 ( 5425) SS BOND : bond 0.00213 / 0.11 ( 5) SS BOND : angle 0.80741 / 0.57 ( 10) hydrogen bonds : bond 0.02568 / 1.76 ( 156) hydrogen bonds : angle 4.92752 / 3.53 ( 438) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7994 (tp) REVERT: B 93 SER cc_start: 0.8321 (t) cc_final: 0.7879 (p) REVERT: B 104 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8119 (pt0) REVERT: B 146 GLN cc_start: 0.7961 (mt0) cc_final: 0.7009 (mt0) outliers start: 10 outliers final: 8 residues processed: 64 average time/residue: 0.7635 time to fit residues: 51.1847 Evaluate side-chains 65 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 108 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.135661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.120735 restraints weight = 14137.631| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.74 r_work: 0.3236 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3994 Z= 0.164 Angle : 0.531 4.998 5435 Z= 0.272 Chirality : 0.046 0.147 612 Planarity : 0.004 0.031 690 Dihedral : 4.431 24.480 544 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.75 % Allowed : 12.36 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.40), residues: 491 helix: -1.03 (1.26), residues: 15 sheet: 0.68 (0.33), residues: 259 loop : 0.13 (0.46), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 141 TYR 0.011 0.001 TYR C 121 PHE 0.009 0.001 PHE C 37 TRP 0.005 0.001 TRP A 104 HIS 0.003 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 ( 3989) covalent geometry : angle 0.52940 / 0.27 ( 5425) SS BOND : bond 0.00330 / 0.18 ( 5) SS BOND : angle 1.06090 / 0.78 ( 10) hydrogen bonds : bond 0.02815 / 1.90 ( 156) hydrogen bonds : angle 5.12245 / 3.67 ( 438) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8004 (tp) REVERT: B 93 SER cc_start: 0.8323 (t) cc_final: 0.7886 (p) REVERT: B 104 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8110 (pt0) REVERT: B 141 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7289 (ttm-80) REVERT: B 146 GLN cc_start: 0.8014 (mt0) cc_final: 0.7077 (mt0) outliers start: 12 outliers final: 8 residues processed: 63 average time/residue: 0.7848 time to fit residues: 51.8497 Evaluate side-chains 68 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 108 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.137232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.122555 restraints weight = 14070.138| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.71 r_work: 0.3259 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3994 Z= 0.124 Angle : 0.509 5.032 5435 Z= 0.260 Chirality : 0.045 0.144 612 Planarity : 0.003 0.032 690 Dihedral : 4.311 23.019 544 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.52 % Allowed : 13.04 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.40), residues: 491 helix: -0.83 (1.30), residues: 15 sheet: 0.70 (0.33), residues: 259 loop : 0.14 (0.47), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 115 TYR 0.010 0.001 TYR C 121 PHE 0.008 0.001 PHE C 37 TRP 0.005 0.001 TRP A 160 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 ( 3989) covalent geometry : angle 0.50784 / 0.26 ( 5425) SS BOND : bond 0.00246 / 0.13 ( 5) SS BOND : angle 0.93025 / 0.67 ( 10) hydrogen bonds : bond 0.02632 / 1.79 ( 156) hydrogen bonds : angle 5.01320 / 3.59 ( 438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2720.20 seconds wall clock time: 46 minutes 47.06 seconds (2807.06 seconds total)