Starting phenix.real_space_refine on Tue Aug 4 15:53:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rh7_53960/08_2026/9rh7_53960.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rh7_53960/08_2026/9rh7_53960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rh7_53960/08_2026/9rh7_53960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rh7_53960/08_2026/9rh7_53960.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rh7_53960/08_2026/9rh7_53960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rh7_53960/08_2026/9rh7_53960.map" } resolution = 3.7 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 2965 2.51 5 N 740 2.21 5 O 826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 4550 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2827 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 15, 'TRANS': 362} 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} Time building chain proxies: 0.99, per 1000 atoms: 0.22 Number of scatterers: 4550 At special positions: 0 Unit cell: (67.797, 77.004, 101.277, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 826 8.00 N 740 7.00 C 2965 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: 0.47 Conformation dependent library (CDL) restraints added in 184.9 milliseconds 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1092 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 6 sheets defined 51.7% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 13 through 31 removed outlier: 3.526A pdb=" N ASN A 30 " --> pdb=" O MET A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 44 Processing helix chain 'A' and resid 59 through 85 removed outlier: 3.816A pdb=" N ALA A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 117 removed outlier: 5.026A pdb=" N PHE A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix removed outlier: 3.602A pdb=" N VAL A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix removed outlier: 4.408A pdb=" N PHE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.983A 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 removed outlier: 3.555A pdb=" N LYS A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 200 Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.642A pdb=" N TYR A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.996A pdb=" N GLY A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.525A 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: 3.663A pdb=" N VAL A 330 " --> pdb=" O GLN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 354 through 384 removed outlier: 3.650A pdb=" N VAL A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.555A pdb=" N PHE C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) 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 removed outlier: 3.585A pdb=" N THR B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.525A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.650A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.727A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 807 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: 0.47 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1417 1.34 - 1.46: 1103 1.46 - 1.58: 2099 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 4650 Sorted by residual: bond pdb=" CA ASP B 104 " pdb=" CB ASP B 104 " ideal model delta sigma weight residual 1.513 1.552 -0.039 2.59e-02 1.49e+03 2.22e+00 bond pdb=" C THR C 7 " pdb=" N PRO C 8 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.08e+00 bond pdb=" CA VAL A 219 " pdb=" C VAL A 219 " ideal model delta sigma weight residual 1.530 1.520 0.010 1.12e-02 7.97e+03 7.76e-01 bond pdb=" CA ASP B 104 " pdb=" C ASP B 104 " ideal model delta sigma weight residual 1.532 1.542 -0.010 1.12e-02 7.97e+03 7.30e-01 bond pdb=" C ILE C 29 " pdb=" O ILE C 29 " ideal model delta sigma weight residual 1.242 1.232 0.010 1.17e-02 7.31e+03 7.10e-01 ... (remaining 4645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 6146 1.40 - 2.80: 140 2.80 - 4.20: 27 4.20 - 5.61: 9 5.61 - 7.01: 5 Bond angle restraints: 6327 Sorted by residual: angle pdb=" CA ASP B 104 " pdb=" CB ASP B 104 " pdb=" CG ASP B 104 " ideal model delta sigma weight residual 112.60 115.60 -3.00 1.00e+00 1.00e+00 9.03e+00 angle pdb=" CA ILE C 48 " pdb=" CB ILE C 48 " pdb=" CG1 ILE C 48 " ideal model delta sigma weight residual 110.40 114.46 -4.06 1.70e+00 3.46e-01 5.71e+00 angle pdb=" C ILE A 106 " pdb=" N VAL A 107 " pdb=" CA VAL A 107 " ideal model delta sigma weight residual 120.33 122.17 -1.84 8.00e-01 1.56e+00 5.26e+00 angle pdb=" N GLY B 111 " pdb=" CA GLY B 111 " pdb=" C GLY B 111 " ideal model delta sigma weight residual 112.68 115.54 -2.86 1.26e+00 6.30e-01 5.17e+00 angle pdb=" C VAL A 107 " pdb=" CA VAL A 107 " pdb=" CB VAL A 107 " ideal model delta sigma weight residual 114.00 111.16 2.84 1.31e+00 5.83e-01 4.69e+00 ... (remaining 6322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 2456 15.97 - 31.94: 201 31.94 - 47.91: 56 47.91 - 63.88: 9 63.88 - 79.85: 2 Dihedral angle restraints: 2724 sinusoidal: 1010 harmonic: 1714 Sorted by residual: 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 60.18 32.82 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CA ASN B 103 " pdb=" C ASN B 103 " pdb=" N ASP B 104 " pdb=" CA ASP B 104 " 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 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 65.02 27.98 1 1.00e+01 1.00e-02 1.12e+01 ... (remaining 2721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 523 0.035 - 0.069: 164 0.069 - 0.104: 50 0.104 - 0.139: 12 0.139 - 0.173: 2 Chirality restraints: 751 Sorted by residual: chirality pdb=" CA THR C 7 " pdb=" N THR C 7 " pdb=" C THR C 7 " pdb=" CB THR C 7 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CA ILE B 51 " pdb=" N ILE B 51 " pdb=" C ILE B 51 " pdb=" CB ILE B 51 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA PHE A 96 " pdb=" N PHE A 96 " pdb=" C PHE A 96 " pdb=" CB PHE A 96 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 748 not shown) Planarity restraints: 779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 256 " -0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO A 257 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 148 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO A 149 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 44 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C THR A 44 " 0.020 2.00e-02 2.50e+03 pdb=" O THR A 44 " -0.007 2.00e-02 2.50e+03 pdb=" N PRO A 45 " -0.007 2.00e-02 2.50e+03 ... (remaining 776 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 37 2.59 - 3.17: 3751 3.17 - 3.75: 7044 3.75 - 4.32: 9638 4.32 - 4.90: 16440 Nonbonded interactions: 36910 Sorted by model distance: nonbonded pdb=" OD1 ASP B 104 " pdb=" N PHE B 105 " model vdw 2.013 3.120 nonbonded pdb=" O GLU A 124 " pdb=" OH TYR A 175 " model vdw 2.261 3.040 nonbonded pdb=" OG SER A 387 " pdb=" OE2 GLU B 33 " model vdw 2.274 3.040 nonbonded pdb=" OG SER A 13 " pdb=" OH TYR A 261 " model vdw 2.284 3.040 nonbonded pdb=" NZ LYS A 57 " pdb=" O LEU A 220 " model vdw 2.296 3.120 ... (remaining 36905 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 group one per residue 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.180 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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 0.039 4652 Z= 0.145 Angle : 0.579 7.007 6331 Z= 0.319 Chirality : 0.039 0.173 751 Planarity : 0.004 0.050 779 Dihedral : 13.157 79.851 1626 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.62 % Allowed : 10.17 % Favored : 89.21 % 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: 0.72 (0.34), residues: 596 helix: 0.68 (0.29), residues: 286 sheet: 0.69 (0.46), residues: 121 loop : 0.27 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 46 TYR 0.012 0.001 TYR B 107 PHE 0.008 0.001 PHE A 71 TRP 0.008 0.001 TRP A 379 HIS 0.003 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 4650) covalent geometry : angle 0.57870 / 0.32 ( 6327) SS BOND : bond 0.00194 / 0.09 ( 2) SS BOND : angle 0.20954 / 0.12 ( 4) hydrogen bonds : bond 0.22027 / 14.59 ( 282) hydrogen bonds : angle 8.19897 / 6.00 ( 807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.161 Fit side-chains REVERT: A 302 LEU cc_start: 0.8684 (tp) cc_final: 0.8406 (tt) outliers start: 3 outliers final: 3 residues processed: 58 average time/residue: 0.0815 time to fit residues: 6.0396 Evaluate side-chains 58 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 106 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 20.0000 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.197797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.136912 restraints weight = 5810.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.140812 restraints weight = 2984.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.143438 restraints weight = 1998.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144427 restraints weight = 1579.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.145290 restraints weight = 1405.522| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4652 Z= 0.148 Angle : 0.552 5.877 6331 Z= 0.286 Chirality : 0.041 0.170 751 Planarity : 0.004 0.033 779 Dihedral : 5.116 43.410 648 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.45 % Allowed : 9.54 % Favored : 89.00 % 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: 1.59 (0.34), residues: 596 helix: 1.71 (0.29), residues: 279 sheet: 0.97 (0.47), residues: 121 loop : 0.30 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 46 TYR 0.012 0.001 TYR B 94 PHE 0.011 0.001 PHE A 136 TRP 0.010 0.001 TRP A 379 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 4650) covalent geometry : angle 0.55086 / 0.29 ( 6327) SS BOND : bond 0.00330 / 0.16 ( 2) SS BOND : angle 1.41005 / 1.18 ( 4) hydrogen bonds : bond 0.04197 / 2.87 ( 282) hydrogen bonds : angle 5.35271 / 3.91 ( 807) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.169 Fit side-chains REVERT: A 47 GLN cc_start: 0.7589 (tt0) cc_final: 0.6976 (pm20) outliers start: 7 outliers final: 6 residues processed: 70 average time/residue: 0.0664 time to fit residues: 6.2108 Evaluate side-chains 61 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 318 HIS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 39 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.199547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146055 restraints weight = 5874.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.147772 restraints weight = 3055.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146951 restraints weight = 2049.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147404 restraints weight = 2150.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.148291 restraints weight = 1890.291| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4652 Z= 0.136 Angle : 0.527 5.631 6331 Z= 0.270 Chirality : 0.040 0.169 751 Planarity : 0.004 0.027 779 Dihedral : 4.298 16.988 641 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.49 % Allowed : 11.41 % Favored : 86.10 % 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: 1.69 (0.34), residues: 596 helix: 1.83 (0.29), residues: 280 sheet: 1.09 (0.47), residues: 119 loop : 0.22 (0.47), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 66 TYR 0.015 0.001 TYR B 107 PHE 0.009 0.001 PHE A 72 TRP 0.008 0.001 TRP A 379 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4650) covalent geometry : angle 0.52640 / 0.27 ( 6327) SS BOND : bond 0.00161 / 0.08 ( 2) SS BOND : angle 1.24207 / 1.11 ( 4) hydrogen bonds : bond 0.03711 / 2.51 ( 282) hydrogen bonds : angle 5.00747 / 3.63 ( 807) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.188 Fit side-chains REVERT: A 47 GLN cc_start: 0.7498 (tt0) cc_final: 0.6933 (pm20) REVERT: A 313 ARG cc_start: 0.7362 (tpt170) cc_final: 0.6635 (ttt180) outliers start: 12 outliers final: 9 residues processed: 67 average time/residue: 0.0766 time to fit residues: 6.6833 Evaluate side-chains 65 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 318 HIS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 55 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 8 optimal weight: 0.0670 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 23 optimal weight: 0.0270 chunk 26 optimal weight: 0.0370 chunk 37 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 overall best weight: 0.3054 ------------------------------------------------------------------------------- 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 = 0.4243 r_free = 0.4243 target = 0.203709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149917 restraints weight = 5818.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.149258 restraints weight = 4396.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.150723 restraints weight = 2929.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.150808 restraints weight = 2159.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.151412 restraints weight = 1876.297| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4652 Z= 0.098 Angle : 0.494 5.478 6331 Z= 0.254 Chirality : 0.039 0.163 751 Planarity : 0.003 0.029 779 Dihedral : 4.069 16.750 641 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.24 % Allowed : 14.11 % Favored : 84.65 % 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: 1.97 (0.34), residues: 596 helix: 2.09 (0.29), residues: 280 sheet: 1.26 (0.46), residues: 118 loop : 0.28 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 46 TYR 0.014 0.001 TYR B 107 PHE 0.007 0.001 PHE C 98 TRP 0.008 0.001 TRP A 62 HIS 0.002 0.000 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 4650) covalent geometry : angle 0.49409 / 0.25 ( 6327) SS BOND : bond 0.00173 / 0.08 ( 2) SS BOND : angle 0.71438 / 0.69 ( 4) hydrogen bonds : bond 0.03105 / 2.11 ( 282) hydrogen bonds : angle 4.73264 / 3.42 ( 807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.161 Fit side-chains REVERT: A 47 GLN cc_start: 0.7469 (tt0) cc_final: 0.6920 (pm20) REVERT: A 274 VAL cc_start: 0.8572 (t) cc_final: 0.8368 (p) REVERT: A 313 ARG cc_start: 0.7306 (tpt170) cc_final: 0.6760 (ttt180) REVERT: B 60 TYR cc_start: 0.7610 (m-80) cc_final: 0.7263 (m-80) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.0708 time to fit residues: 6.4995 Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 43 optimal weight: 0.0970 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.201569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142867 restraints weight = 5879.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.146549 restraints weight = 3037.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.148991 restraints weight = 2032.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.150039 restraints weight = 1619.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.150834 restraints weight = 1438.891| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4652 Z= 0.100 Angle : 0.490 6.691 6331 Z= 0.248 Chirality : 0.039 0.163 751 Planarity : 0.003 0.028 779 Dihedral : 4.001 16.846 641 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.45 % Allowed : 15.15 % Favored : 83.40 % 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: 2.11 (0.35), residues: 596 helix: 2.25 (0.30), residues: 280 sheet: 1.28 (0.46), residues: 118 loop : 0.31 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 66 TYR 0.011 0.001 TYR B 107 PHE 0.008 0.001 PHE A 72 TRP 0.006 0.001 TRP A 216 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 4650) covalent geometry : angle 0.48955 / 0.25 ( 6327) SS BOND : bond 0.00184 / 0.09 ( 2) SS BOND : angle 0.53262 / 0.49 ( 4) hydrogen bonds : bond 0.03024 / 2.06 ( 282) hydrogen bonds : angle 4.61728 / 3.35 ( 807) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.166 Fit side-chains REVERT: A 47 GLN cc_start: 0.7457 (tt0) cc_final: 0.6948 (pm20) REVERT: A 59 MET cc_start: 0.8731 (tpp) cc_final: 0.8486 (tpp) REVERT: A 313 ARG cc_start: 0.7294 (tpt170) cc_final: 0.6678 (ttt180) REVERT: B 60 TYR cc_start: 0.7558 (m-80) cc_final: 0.7240 (m-80) outliers start: 7 outliers final: 6 residues processed: 63 average time/residue: 0.0810 time to fit residues: 6.5855 Evaluate side-chains 63 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 50 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.200887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.142037 restraints weight = 5988.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.145712 restraints weight = 3098.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.147491 restraints weight = 2069.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.149412 restraints weight = 1679.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.150099 restraints weight = 1484.612| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4652 Z= 0.106 Angle : 0.489 5.551 6331 Z= 0.247 Chirality : 0.039 0.163 751 Planarity : 0.003 0.027 779 Dihedral : 3.948 17.139 641 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.87 % Allowed : 14.94 % Favored : 83.20 % 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: 2.23 (0.35), residues: 596 helix: 2.37 (0.30), residues: 280 sheet: 1.33 (0.47), residues: 118 loop : 0.33 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 66 TYR 0.011 0.001 TYR B 107 PHE 0.009 0.001 PHE A 72 TRP 0.005 0.001 TRP A 216 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 4650) covalent geometry : angle 0.48890 / 0.25 ( 6327) SS BOND : bond 0.00176 / 0.08 ( 2) SS BOND : angle 0.52700 / 0.48 ( 4) hydrogen bonds : bond 0.02966 / 2.03 ( 282) hydrogen bonds : angle 4.54436 / 3.29 ( 807) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.162 Fit side-chains REVERT: A 47 GLN cc_start: 0.7440 (tt0) cc_final: 0.6939 (pm20) REVERT: A 313 ARG cc_start: 0.7300 (tpt170) cc_final: 0.6866 (ttt-90) REVERT: B 60 TYR cc_start: 0.7627 (m-80) cc_final: 0.7340 (m-80) outliers start: 9 outliers final: 7 residues processed: 64 average time/residue: 0.0748 time to fit residues: 6.1687 Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 4.9990 chunk 43 optimal weight: 0.0010 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 0.0370 overall best weight: 0.5266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.202751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144527 restraints weight = 5840.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.148334 restraints weight = 3012.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.150855 restraints weight = 2015.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.151850 restraints weight = 1610.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.152260 restraints weight = 1437.018| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4652 Z= 0.096 Angle : 0.479 5.621 6331 Z= 0.241 Chirality : 0.038 0.162 751 Planarity : 0.003 0.028 779 Dihedral : 3.877 16.906 641 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.28 % Allowed : 14.73 % Favored : 82.99 % 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: 2.32 (0.35), residues: 596 helix: 2.45 (0.30), residues: 280 sheet: 1.21 (0.47), residues: 122 loop : 0.46 (0.49), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 66 TYR 0.010 0.001 TYR B 107 PHE 0.007 0.001 PHE A 72 TRP 0.006 0.001 TRP A 216 HIS 0.002 0.000 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 4650) covalent geometry : angle 0.47919 / 0.24 ( 6327) SS BOND : bond 0.00193 / 0.09 ( 2) SS BOND : angle 0.50429 / 0.46 ( 4) hydrogen bonds : bond 0.02810 / 1.93 ( 282) hydrogen bonds : angle 4.46776 / 3.24 ( 807) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.160 Fit side-chains REVERT: A 47 GLN cc_start: 0.7411 (tt0) cc_final: 0.6888 (pm20) REVERT: A 313 ARG cc_start: 0.7312 (tpt170) cc_final: 0.6823 (ttp-170) REVERT: A 366 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8396 (mt) REVERT: B 60 TYR cc_start: 0.7557 (m-80) cc_final: 0.7267 (m-80) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.0738 time to fit residues: 6.3263 Evaluate side-chains 65 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.201660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148189 restraints weight = 5924.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.148315 restraints weight = 3890.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149586 restraints weight = 2458.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.149930 restraints weight = 1929.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.149980 restraints weight = 1734.270| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4652 Z= 0.104 Angle : 0.491 6.054 6331 Z= 0.247 Chirality : 0.039 0.162 751 Planarity : 0.003 0.028 779 Dihedral : 3.875 16.879 641 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.28 % Allowed : 15.15 % Favored : 82.57 % 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: 2.40 (0.35), residues: 596 helix: 2.48 (0.30), residues: 280 sheet: 1.50 (0.47), residues: 118 loop : 0.41 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 66 TYR 0.008 0.001 TYR B 107 PHE 0.008 0.001 PHE A 72 TRP 0.005 0.001 TRP B 36 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 ( 4650) covalent geometry : angle 0.49068 / 0.25 ( 6327) SS BOND : bond 0.00192 / 0.09 ( 2) SS BOND : angle 0.50105 / 0.46 ( 4) hydrogen bonds : bond 0.02831 / 1.95 ( 282) hydrogen bonds : angle 4.45536 / 3.24 ( 807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.195 Fit side-chains REVERT: A 47 GLN cc_start: 0.7279 (tt0) cc_final: 0.6784 (pm20) REVERT: A 313 ARG cc_start: 0.7276 (tpt170) cc_final: 0.6865 (ttp-170) REVERT: A 366 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8458 (mt) REVERT: B 60 TYR cc_start: 0.7599 (m-80) cc_final: 0.7377 (m-80) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 0.0836 time to fit residues: 7.2905 Evaluate side-chains 67 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 34 optimal weight: 0.0060 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.199381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145565 restraints weight = 5883.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.144341 restraints weight = 3907.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.145342 restraints weight = 2995.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145712 restraints weight = 2328.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145962 restraints weight = 2188.019| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4652 Z= 0.133 Angle : 0.530 8.651 6331 Z= 0.262 Chirality : 0.039 0.163 751 Planarity : 0.003 0.027 779 Dihedral : 3.999 16.933 641 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.87 % Allowed : 15.98 % Favored : 82.16 % 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: 2.19 (0.35), residues: 596 helix: 2.20 (0.30), residues: 288 sheet: 1.53 (0.48), residues: 118 loop : 0.30 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 66 TYR 0.009 0.001 TYR A 208 PHE 0.009 0.001 PHE A 72 TRP 0.006 0.001 TRP A 379 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 ( 4650) covalent geometry : angle 0.53049 / 0.26 ( 6327) SS BOND : bond 0.00178 / 0.08 ( 2) SS BOND : angle 0.53604 / 0.50 ( 4) hydrogen bonds : bond 0.03020 / 2.08 ( 282) hydrogen bonds : angle 4.50113 / 3.27 ( 807) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.169 Fit side-chains REVERT: A 47 GLN cc_start: 0.7303 (tt0) cc_final: 0.6848 (pm20) REVERT: A 313 ARG cc_start: 0.7300 (tpt170) cc_final: 0.6871 (ttp-170) outliers start: 9 outliers final: 7 residues processed: 64 average time/residue: 0.0845 time to fit residues: 6.8643 Evaluate side-chains 66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.201120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.142293 restraints weight = 5866.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.146276 restraints weight = 3022.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148826 restraints weight = 2021.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.149732 restraints weight = 1604.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.150464 restraints weight = 1437.795| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4652 Z= 0.106 Angle : 0.509 8.238 6331 Z= 0.252 Chirality : 0.038 0.163 751 Planarity : 0.003 0.028 779 Dihedral : 3.904 16.742 641 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.66 % Allowed : 16.39 % Favored : 81.95 % 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: 2.22 (0.35), residues: 596 helix: 2.30 (0.30), residues: 286 sheet: 1.39 (0.47), residues: 122 loop : 0.29 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 66 TYR 0.008 0.001 TYR A 208 PHE 0.008 0.001 PHE A 72 TRP 0.005 0.001 TRP A 216 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 4650) covalent geometry : angle 0.50875 / 0.25 ( 6327) SS BOND : bond 0.00208 / 0.10 ( 2) SS BOND : angle 0.49200 / 0.45 ( 4) hydrogen bonds : bond 0.02839 / 1.96 ( 282) hydrogen bonds : angle 4.43417 / 3.22 ( 807) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.201 Fit side-chains REVERT: A 47 GLN cc_start: 0.7276 (tt0) cc_final: 0.6795 (pm20) REVERT: A 313 ARG cc_start: 0.7334 (tpt170) cc_final: 0.6843 (ttp-170) REVERT: C 66 ARG cc_start: 0.6924 (tpt-90) cc_final: 0.6644 (ttt90) outliers start: 8 outliers final: 7 residues processed: 64 average time/residue: 0.0807 time to fit residues: 6.7047 Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 9 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.200125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140114 restraints weight = 5895.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.143062 restraints weight = 3183.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.144613 restraints weight = 2223.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.146150 restraints weight = 1822.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146615 restraints weight = 1624.937| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4652 Z= 0.146 Angle : 0.546 8.299 6331 Z= 0.269 Chirality : 0.040 0.163 751 Planarity : 0.003 0.026 779 Dihedral : 4.053 17.622 641 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.28 % Allowed : 16.18 % Favored : 81.54 % 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: 2.12 (0.35), residues: 596 helix: 2.15 (0.30), residues: 288 sheet: 1.50 (0.47), residues: 118 loop : 0.24 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 66 TYR 0.009 0.001 TYR A 208 PHE 0.009 0.001 PHE A 72 TRP 0.007 0.001 TRP A 379 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 4650) covalent geometry : angle 0.54614 / 0.27 ( 6327) SS BOND : bond 0.00193 / 0.09 ( 2) SS BOND : angle 0.57492 / 0.53 ( 4) hydrogen bonds : bond 0.03108 / 2.14 ( 282) hydrogen bonds : angle 4.51190 / 3.28 ( 807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 918.80 seconds wall clock time: 16 minutes 36.26 seconds (996.26 seconds total)