Starting phenix.real_space_refine on Fri Aug 22 13:26:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u3v_63828/08_2025/9u3v_63828.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u3v_63828/08_2025/9u3v_63828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u3v_63828/08_2025/9u3v_63828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u3v_63828/08_2025/9u3v_63828.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u3v_63828/08_2025/9u3v_63828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u3v_63828/08_2025/9u3v_63828.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.051 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 22 5.16 5 C 2261 2.51 5 N 544 2.21 5 O 574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3401 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3401 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain breaks: 6 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 1.22, per 1000 atoms: 0.36 Number of scatterers: 3401 At special positions: 0 Unit cell: (52.52, 75.75, 91.91, 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 22 16.00 O 574 8.00 N 544 7.00 C 2261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.30 Conformation dependent library (CDL) restraints added in 123.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 818 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 89.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 98 through 138 Proline residue: A 110 - end of helix removed outlier: 3.694A pdb=" N PHE A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 131 " --> pdb=" O CYS A 127 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 142 through 165 removed outlier: 3.541A pdb=" N ALA A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Proline residue: A 148 - end of helix removed outlier: 3.575A pdb=" N LEU A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 155 " --> pdb=" O CYS A 151 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 171 Processing helix chain 'A' and resid 171 through 195 removed outlier: 4.155A pdb=" N LEU A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 237 Processing helix chain 'A' and resid 241 through 263 removed outlier: 4.028A pdb=" N TYR A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 324 removed outlier: 3.822A pdb=" N ARG A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 765 Processing helix chain 'A' and resid 765 through 774 Processing helix chain 'A' and resid 782 through 809 removed outlier: 3.671A pdb=" N SER A 787 " --> pdb=" O PRO A 783 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 788 " --> pdb=" O THR A 784 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR A 809 " --> pdb=" O CYS A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 843 removed outlier: 3.843A pdb=" N LEU A 833 " --> pdb=" O LEU A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 860 removed outlier: 3.677A pdb=" N GLU A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP A 858 " --> pdb=" O ARG A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 881 Proline residue: A 876 - end of helix removed outlier: 3.746A pdb=" N VAL A 880 " --> pdb=" O PRO A 876 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 884 No H-bonds generated for 'chain 'A' and resid 882 through 884' Processing helix chain 'A' and resid 896 through 909 removed outlier: 3.949A pdb=" N ILE A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 928 Processing helix chain 'A' and resid 929 through 936 Processing helix chain 'A' and resid 978 through 1024 removed outlier: 4.129A pdb=" N VAL A 983 " --> pdb=" O GLY A 979 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 984 " --> pdb=" O GLN A 980 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 816 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: 0.59 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1018 1.34 - 1.46: 611 1.46 - 1.57: 1832 1.57 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3492 Sorted by residual: bond pdb=" CB ASP A1015 " pdb=" CG ASP A1015 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.29e+00 bond pdb=" CA VAL A 237 " pdb=" C VAL A 237 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.27e-02 6.20e+03 1.22e+00 bond pdb=" C VAL A 237 " pdb=" O VAL A 237 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.18e+00 bond pdb=" CA ASP A1015 " pdb=" CB ASP A1015 " ideal model delta sigma weight residual 1.529 1.545 -0.016 1.74e-02 3.30e+03 8.68e-01 bond pdb=" CA PHE A 894 " pdb=" C PHE A 894 " ideal model delta sigma weight residual 1.525 1.540 -0.015 2.10e-02 2.27e+03 5.24e-01 ... (remaining 3487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 4674 1.40 - 2.80: 51 2.80 - 4.20: 14 4.20 - 5.60: 8 5.60 - 7.00: 1 Bond angle restraints: 4748 Sorted by residual: angle pdb=" CA VAL A 237 " pdb=" CB VAL A 237 " pdb=" CG2 VAL A 237 " ideal model delta sigma weight residual 110.40 114.82 -4.42 1.70e+00 3.46e-01 6.76e+00 angle pdb=" CA ASP A1015 " pdb=" CB ASP A1015 " pdb=" CG ASP A1015 " ideal model delta sigma weight residual 112.60 114.69 -2.09 1.00e+00 1.00e+00 4.36e+00 angle pdb=" CA LEU A 863 " pdb=" CB LEU A 863 " pdb=" CG LEU A 863 " ideal model delta sigma weight residual 116.30 123.30 -7.00 3.50e+00 8.16e-02 4.00e+00 angle pdb=" CA MET A 849 " pdb=" CB MET A 849 " pdb=" CG MET A 849 " ideal model delta sigma weight residual 114.10 117.99 -3.89 2.00e+00 2.50e-01 3.78e+00 angle pdb=" CB ASP A1015 " pdb=" CG ASP A1015 " pdb=" OD1 ASP A1015 " ideal model delta sigma weight residual 118.40 122.61 -4.21 2.30e+00 1.89e-01 3.35e+00 ... (remaining 4743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 1658 16.34 - 32.67: 246 32.67 - 49.01: 94 49.01 - 65.34: 12 65.34 - 81.68: 5 Dihedral angle restraints: 2015 sinusoidal: 760 harmonic: 1255 Sorted by residual: dihedral pdb=" CG ARG A 761 " pdb=" CD ARG A 761 " pdb=" NE ARG A 761 " pdb=" CZ ARG A 761 " ideal model delta sinusoidal sigma weight residual -90.00 -131.78 41.78 2 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB MET A1024 " pdb=" CG MET A1024 " pdb=" SD MET A1024 " pdb=" CE MET A1024 " ideal model delta sinusoidal sigma weight residual -60.00 -114.84 54.84 3 1.50e+01 4.44e-03 9.31e+00 dihedral pdb=" CA LEU A 829 " pdb=" CB LEU A 829 " pdb=" CG LEU A 829 " pdb=" CD1 LEU A 829 " ideal model delta sinusoidal sigma weight residual 180.00 125.29 54.71 3 1.50e+01 4.44e-03 9.30e+00 ... (remaining 2012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 539 0.075 - 0.151: 20 0.151 - 0.226: 0 0.226 - 0.301: 0 0.301 - 0.377: 1 Chirality restraints: 560 Sorted by residual: chirality pdb=" CB VAL A 237 " pdb=" CA VAL A 237 " pdb=" CG1 VAL A 237 " pdb=" CG2 VAL A 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA ILE A 747 " pdb=" N ILE A 747 " pdb=" C ILE A 747 " pdb=" CB ILE A 747 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ASP A1015 " pdb=" N ASP A1015 " pdb=" C ASP A1015 " pdb=" CB ASP A1015 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 557 not shown) Planarity restraints: 573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 240 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 241 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 147 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO A 148 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 148 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 148 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 930 " 0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO A 931 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 931 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 931 " 0.017 5.00e-02 4.00e+02 ... (remaining 570 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 465 2.75 - 3.29: 3521 3.29 - 3.82: 5698 3.82 - 4.36: 6635 4.36 - 4.90: 11254 Nonbonded interactions: 27573 Sorted by model distance: nonbonded pdb=" OG SER A 787 " pdb=" OE1 GLN A 914 " model vdw 2.211 3.040 nonbonded pdb=" ND2 ASN A 748 " pdb=" OG SER A 751 " model vdw 2.327 3.120 nonbonded pdb=" O GLY A 222 " pdb=" OG SER A 225 " model vdw 2.337 3.040 nonbonded pdb=" NH2 ARG A 141 " pdb=" O VAL A 194 " model vdw 2.379 3.120 nonbonded pdb=" OG SER A 874 " pdb=" OH TYR A 909 " model vdw 2.379 3.040 ... (remaining 27568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.280 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3492 Z= 0.103 Angle : 0.455 6.999 4748 Z= 0.233 Chirality : 0.037 0.377 560 Planarity : 0.004 0.037 573 Dihedral : 17.953 81.675 1197 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 31.81 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.43), residues: 412 helix: 0.60 (0.28), residues: 343 sheet: None (None), residues: 0 loop : 0.24 (0.90), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 840 TYR 0.006 0.001 TYR A 881 PHE 0.009 0.001 PHE A 785 TRP 0.003 0.001 TRP A 130 HIS 0.002 0.001 HIS A1007 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 3492) covalent geometry : angle 0.45539 ( 4748) hydrogen bonds : bond 0.25785 ( 272) hydrogen bonds : angle 8.02738 ( 816) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.127 Fit side-chains REVERT: A 316 SER cc_start: 0.8673 (m) cc_final: 0.8388 (p) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0583 time to fit residues: 5.6816 Evaluate side-chains 76 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 908 HIS ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.152533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.137823 restraints weight = 4225.906| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.70 r_work: 0.3737 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3492 Z= 0.179 Angle : 0.547 5.830 4748 Z= 0.298 Chirality : 0.039 0.153 560 Planarity : 0.005 0.036 573 Dihedral : 3.966 15.858 455 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.77 % Allowed : 28.03 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.42), residues: 412 helix: 1.83 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.24 (0.98), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 840 TYR 0.010 0.001 TYR A1004 PHE 0.026 0.001 PHE A 152 TRP 0.007 0.001 TRP A 858 HIS 0.003 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 3492) covalent geometry : angle 0.54685 ( 4748) hydrogen bonds : bond 0.05770 ( 272) hydrogen bonds : angle 4.76868 ( 816) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.098 Fit side-chains REVERT: A 122 TYR cc_start: 0.8568 (t80) cc_final: 0.7785 (t80) REVERT: A 229 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7655 (mt-10) REVERT: A 232 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8420 (m-80) outliers start: 14 outliers final: 8 residues processed: 101 average time/residue: 0.0648 time to fit residues: 7.7238 Evaluate side-chains 95 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 907 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 0.0570 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.152624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.137470 restraints weight = 4273.039| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.72 r_work: 0.3751 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3492 Z= 0.124 Angle : 0.491 6.861 4748 Z= 0.260 Chirality : 0.039 0.272 560 Planarity : 0.004 0.039 573 Dihedral : 3.797 15.019 455 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.70 % Allowed : 28.30 % Favored : 69.00 % 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 aren not related in a simple way. whole: 3.06 (0.42), residues: 412 helix: 2.39 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.22 (0.98), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.010 0.001 TYR A 881 PHE 0.018 0.001 PHE A 987 TRP 0.009 0.001 TRP A 994 HIS 0.002 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3492) covalent geometry : angle 0.49121 ( 4748) hydrogen bonds : bond 0.04673 ( 272) hydrogen bonds : angle 4.24092 ( 816) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.130 Fit side-chains REVERT: A 316 SER cc_start: 0.8645 (m) cc_final: 0.8303 (p) REVERT: A 769 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6899 (mm-30) REVERT: A 878 LEU cc_start: 0.8398 (mp) cc_final: 0.8120 (mp) REVERT: A 1020 LYS cc_start: 0.8065 (mptt) cc_final: 0.7674 (mptt) outliers start: 10 outliers final: 6 residues processed: 97 average time/residue: 0.0739 time to fit residues: 8.4443 Evaluate side-chains 86 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 991 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 22 optimal weight: 0.0870 chunk 28 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 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 = 0.4063 r_free = 0.4063 target = 0.152779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.137658 restraints weight = 4225.860| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.70 r_work: 0.3750 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3492 Z= 0.127 Angle : 0.487 7.065 4748 Z= 0.259 Chirality : 0.039 0.272 560 Planarity : 0.004 0.040 573 Dihedral : 3.735 15.071 455 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.50 % Allowed : 28.57 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.15 (0.43), residues: 412 helix: 2.44 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -0.40 (1.05), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 840 TYR 0.008 0.001 TYR A 881 PHE 0.016 0.001 PHE A 152 TRP 0.008 0.001 TRP A 994 HIS 0.002 0.001 HIS A1007 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 3492) covalent geometry : angle 0.48687 ( 4748) hydrogen bonds : bond 0.04300 ( 272) hydrogen bonds : angle 4.04271 ( 816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 769 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6939 (mm-30) REVERT: A 878 LEU cc_start: 0.8371 (mp) cc_final: 0.8091 (mp) REVERT: A 911 ASN cc_start: 0.8478 (t0) cc_final: 0.8278 (t0) REVERT: A 1020 LYS cc_start: 0.8053 (mptt) cc_final: 0.7695 (mptt) outliers start: 13 outliers final: 9 residues processed: 89 average time/residue: 0.0783 time to fit residues: 8.2593 Evaluate side-chains 86 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1024 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 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 = 0.4046 r_free = 0.4046 target = 0.151646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.136829 restraints weight = 4300.549| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.72 r_work: 0.3737 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3492 Z= 0.143 Angle : 0.498 7.146 4748 Z= 0.263 Chirality : 0.040 0.291 560 Planarity : 0.004 0.043 573 Dihedral : 3.743 15.552 455 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.50 % Allowed : 28.57 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.15 (0.43), residues: 412 helix: 2.41 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.29 (1.05), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 840 TYR 0.008 0.001 TYR A 881 PHE 0.010 0.001 PHE A 134 TRP 0.006 0.001 TRP A 994 HIS 0.003 0.001 HIS A1007 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3492) covalent geometry : angle 0.49812 ( 4748) hydrogen bonds : bond 0.04336 ( 272) hydrogen bonds : angle 4.01634 ( 816) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: A 878 LEU cc_start: 0.8366 (mp) cc_final: 0.8106 (mp) REVERT: A 1004 TYR cc_start: 0.8497 (t80) cc_final: 0.8290 (t80) REVERT: A 1020 LYS cc_start: 0.8063 (mptt) cc_final: 0.7693 (mptt) outliers start: 13 outliers final: 11 residues processed: 92 average time/residue: 0.0605 time to fit residues: 6.6288 Evaluate side-chains 91 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1024 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 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 = 0.4045 r_free = 0.4045 target = 0.151396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.136988 restraints weight = 4268.211| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.63 r_work: 0.3746 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3492 Z= 0.145 Angle : 0.504 7.047 4748 Z= 0.268 Chirality : 0.040 0.299 560 Planarity : 0.004 0.044 573 Dihedral : 3.725 15.874 455 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.77 % Allowed : 28.57 % Favored : 67.65 % 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 aren not related in a simple way. whole: 3.12 (0.43), residues: 412 helix: 2.41 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.38 (1.03), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 840 TYR 0.008 0.001 TYR A 881 PHE 0.021 0.001 PHE A 152 TRP 0.006 0.001 TRP A 994 HIS 0.002 0.001 HIS A1007 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3492) covalent geometry : angle 0.50383 ( 4748) hydrogen bonds : bond 0.04294 ( 272) hydrogen bonds : angle 3.95918 ( 816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 145 MET cc_start: 0.5904 (ttp) cc_final: 0.5532 (ttp) REVERT: A 878 LEU cc_start: 0.8397 (mp) cc_final: 0.8134 (mp) REVERT: A 1004 TYR cc_start: 0.8467 (t80) cc_final: 0.8258 (t80) REVERT: A 1020 LYS cc_start: 0.8013 (mptt) cc_final: 0.7657 (mptt) outliers start: 14 outliers final: 12 residues processed: 90 average time/residue: 0.0759 time to fit residues: 8.0705 Evaluate side-chains 90 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1024 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.152507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.137688 restraints weight = 4350.238| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.73 r_work: 0.3755 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3492 Z= 0.126 Angle : 0.506 6.937 4748 Z= 0.267 Chirality : 0.037 0.157 560 Planarity : 0.004 0.044 573 Dihedral : 3.664 16.173 455 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.96 % Allowed : 28.30 % Favored : 68.73 % 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 aren not related in a simple way. whole: 3.30 (0.43), residues: 412 helix: 2.52 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -0.26 (1.03), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 840 TYR 0.007 0.001 TYR A1004 PHE 0.008 0.001 PHE A1000 TRP 0.007 0.001 TRP A 994 HIS 0.002 0.000 HIS A1007 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3492) covalent geometry : angle 0.50569 ( 4748) hydrogen bonds : bond 0.04074 ( 272) hydrogen bonds : angle 3.90764 ( 816) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: A 227 CYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7700 (p) REVERT: A 878 LEU cc_start: 0.8386 (mp) cc_final: 0.8129 (mp) REVERT: A 1020 LYS cc_start: 0.8011 (mptt) cc_final: 0.7637 (mptt) outliers start: 11 outliers final: 9 residues processed: 86 average time/residue: 0.0647 time to fit residues: 6.6727 Evaluate side-chains 86 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1024 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.151809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.137316 restraints weight = 4390.593| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.66 r_work: 0.3753 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3492 Z= 0.143 Angle : 0.537 6.902 4748 Z= 0.285 Chirality : 0.040 0.316 560 Planarity : 0.004 0.045 573 Dihedral : 3.675 16.432 455 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.96 % Allowed : 28.30 % Favored : 68.73 % 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 aren not related in a simple way. whole: 3.17 (0.43), residues: 412 helix: 2.45 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.45 (1.02), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 840 TYR 0.008 0.001 TYR A 881 PHE 0.009 0.001 PHE A 785 TRP 0.006 0.001 TRP A 994 HIS 0.003 0.001 HIS A1007 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 3492) covalent geometry : angle 0.53655 ( 4748) hydrogen bonds : bond 0.04174 ( 272) hydrogen bonds : angle 3.88672 ( 816) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.6492 (ptp) cc_final: 0.6271 (ptm) REVERT: A 878 LEU cc_start: 0.8416 (mp) cc_final: 0.8163 (mp) REVERT: A 1004 TYR cc_start: 0.8442 (t80) cc_final: 0.8188 (t80) outliers start: 11 outliers final: 10 residues processed: 87 average time/residue: 0.0746 time to fit residues: 7.5892 Evaluate side-chains 89 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1024 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.151527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.137083 restraints weight = 4286.197| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.69 r_work: 0.3749 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3492 Z= 0.147 Angle : 0.532 7.737 4748 Z= 0.277 Chirality : 0.038 0.149 560 Planarity : 0.004 0.044 573 Dihedral : 3.702 16.456 455 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.23 % Allowed : 28.03 % Favored : 68.73 % 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 aren not related in a simple way. whole: 3.11 (0.43), residues: 412 helix: 2.42 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.57 (0.99), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 840 TYR 0.007 0.001 TYR A 881 PHE 0.008 0.001 PHE A 785 TRP 0.005 0.001 TRP A 994 HIS 0.003 0.001 HIS A1007 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3492) covalent geometry : angle 0.53183 ( 4748) hydrogen bonds : bond 0.04204 ( 272) hydrogen bonds : angle 3.92937 ( 816) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 878 LEU cc_start: 0.8401 (mp) cc_final: 0.8149 (mp) REVERT: A 1004 TYR cc_start: 0.8420 (t80) cc_final: 0.8155 (t80) outliers start: 12 outliers final: 11 residues processed: 89 average time/residue: 0.0678 time to fit residues: 7.1382 Evaluate side-chains 91 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1024 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 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 = 0.4054 r_free = 0.4054 target = 0.151877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.137313 restraints weight = 4264.466| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.69 r_work: 0.3753 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3492 Z= 0.139 Angle : 0.539 7.062 4748 Z= 0.283 Chirality : 0.041 0.323 560 Planarity : 0.004 0.043 573 Dihedral : 3.718 16.655 455 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.70 % Allowed : 29.11 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.12 (0.43), residues: 412 helix: 2.44 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -0.65 (1.01), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 305 TYR 0.007 0.001 TYR A1004 PHE 0.012 0.001 PHE A 785 TRP 0.006 0.001 TRP A 994 HIS 0.002 0.001 HIS A1007 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3492) covalent geometry : angle 0.53887 ( 4748) hydrogen bonds : bond 0.04137 ( 272) hydrogen bonds : angle 3.90340 ( 816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 227 CYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7672 (p) REVERT: A 878 LEU cc_start: 0.8384 (mp) cc_final: 0.8134 (mp) REVERT: A 1004 TYR cc_start: 0.8412 (t80) cc_final: 0.8169 (t80) outliers start: 10 outliers final: 9 residues processed: 88 average time/residue: 0.0696 time to fit residues: 7.3147 Evaluate side-chains 89 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1024 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 911 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 = 0.4066 r_free = 0.4066 target = 0.152725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.137932 restraints weight = 4367.254| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.72 r_work: 0.3761 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3492 Z= 0.122 Angle : 0.533 8.854 4748 Z= 0.275 Chirality : 0.037 0.166 560 Planarity : 0.004 0.044 573 Dihedral : 3.631 16.475 455 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.96 % Allowed : 28.84 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.25 (0.43), residues: 412 helix: 2.53 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -0.59 (1.01), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 840 TYR 0.006 0.001 TYR A1004 PHE 0.009 0.001 PHE A 785 TRP 0.006 0.001 TRP A 994 HIS 0.002 0.000 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 3492) covalent geometry : angle 0.53336 ( 4748) hydrogen bonds : bond 0.03873 ( 272) hydrogen bonds : angle 3.85043 ( 816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 894.37 seconds wall clock time: 16 minutes 2.08 seconds (962.08 seconds total)