Starting phenix.real_space_refine on Thu Jul 2 03:27:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lrc_23494/07_2026/7lrc_23494.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lrc_23494/07_2026/7lrc_23494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lrc_23494/07_2026/7lrc_23494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lrc_23494/07_2026/7lrc_23494.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lrc_23494/07_2026/7lrc_23494.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lrc_23494/07_2026/7lrc_23494.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lrc_23494/07_2026/7lrc_23494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lrc_23494/07_2026/7lrc_23494.map" } resolution = 2.97 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: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 Mg 2 5.21 5 S 36 5.16 5 C 3996 2.51 5 N 1040 2.21 5 O 1126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6202 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2998 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 18, 'TRANS': 352} Chain breaks: 2 Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 79 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 1, ' MN': 1, 'X5M': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: C, D Time building chain proxies: 2.08, per 1000 atoms: 0.34 Number of scatterers: 6202 At special positions: 0 Unit cell: (115.867, 94.607, 74.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 36 16.00 Mg 2 11.99 O 1126 8.00 N 1040 7.00 C 3996 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: 0.53 Conformation dependent library (CDL) restraints added in 436.6 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 73.8% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'B' and resid 679 through 683 removed outlier: 3.621A pdb=" N LEU B 682 " --> pdb=" O MET B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 691 removed outlier: 4.162A pdb=" N ASN B 690 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 691 " --> pdb=" O GLN B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 704 Processing helix chain 'B' and resid 709 through 723 Processing helix chain 'B' and resid 723 through 728 Processing helix chain 'B' and resid 731 through 746 Processing helix chain 'B' and resid 753 through 770 Processing helix chain 'B' and resid 816 through 820 Processing helix chain 'B' and resid 822 through 836 Processing helix chain 'B' and resid 844 through 851 Processing helix chain 'B' and resid 853 through 859 Processing helix chain 'B' and resid 863 through 880 removed outlier: 4.034A pdb=" N ARG B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 884 Processing helix chain 'B' and resid 890 through 908 removed outlier: 3.679A pdb=" N THR B 908 " --> pdb=" O ALA B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 926 Processing helix chain 'B' and resid 934 through 951 removed outlier: 3.585A pdb=" N ILE B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 956 Processing helix chain 'B' and resid 957 through 983 Processing helix chain 'B' and resid 996 through 1008 Processing helix chain 'B' and resid 1008 through 1020 Processing helix chain 'B' and resid 1073 through 1100 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'C' and resid 679 through 683 removed outlier: 3.621A pdb=" N LEU C 682 " --> pdb=" O MET C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 691 removed outlier: 4.163A pdb=" N ASN C 690 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR C 691 " --> pdb=" O GLN C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 704 Processing helix chain 'C' and resid 709 through 723 Processing helix chain 'C' and resid 723 through 728 Processing helix chain 'C' and resid 731 through 746 Processing helix chain 'C' and resid 753 through 770 Processing helix chain 'C' and resid 816 through 820 Processing helix chain 'C' and resid 822 through 836 Processing helix chain 'C' and resid 844 through 851 Processing helix chain 'C' and resid 853 through 859 Processing helix chain 'C' and resid 863 through 880 removed outlier: 4.034A pdb=" N ARG C 880 " --> pdb=" O LEU C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 884 Processing helix chain 'C' and resid 890 through 908 removed outlier: 3.679A pdb=" N THR C 908 " --> pdb=" O ALA C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 926 Processing helix chain 'C' and resid 934 through 951 removed outlier: 3.585A pdb=" N ILE C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 952 through 956 Processing helix chain 'C' and resid 957 through 983 Processing helix chain 'C' and resid 996 through 1008 Processing helix chain 'C' and resid 1008 through 1020 Processing helix chain 'C' and resid 1073 through 1100 Processing helix chain 'D' and resid 552 through 559 Processing sheet with id=AA1, first strand: chain 'B' and resid 772 through 773 Processing sheet with id=AA2, first strand: chain 'B' and resid 1025 through 1027 removed outlier: 3.505A pdb=" N LYS B1070 " --> pdb=" O VAL B1027 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 772 through 773 Processing sheet with id=AA4, first strand: chain 'C' and resid 1025 through 1027 removed outlier: 3.505A pdb=" N LYS C1070 " --> pdb=" O VAL C1027 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1278 1.33 - 1.45: 1530 1.45 - 1.57: 3492 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6358 Sorted by residual: bond pdb=" N16 X5M C2003 " pdb=" N17 X5M C2003 " ideal model delta sigma weight residual 1.354 1.394 -0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" N16 X5M B2003 " pdb=" N17 X5M B2003 " ideal model delta sigma weight residual 1.354 1.394 -0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" C15 X5M C2003 " pdb=" C21 X5M C2003 " ideal model delta sigma weight residual 1.505 1.544 -0.039 2.00e-02 2.50e+03 3.73e+00 bond pdb=" C15 X5M B2003 " pdb=" C21 X5M B2003 " ideal model delta sigma weight residual 1.505 1.544 -0.039 2.00e-02 2.50e+03 3.73e+00 bond pdb=" C11 X5M C2003 " pdb=" N12 X5M C2003 " ideal model delta sigma weight residual 1.454 1.427 0.027 2.00e-02 2.50e+03 1.81e+00 ... (remaining 6353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 8550 2.15 - 4.29: 68 4.29 - 6.44: 10 6.44 - 8.59: 0 8.59 - 10.74: 2 Bond angle restraints: 8630 Sorted by residual: angle pdb=" C05 X5M B2003 " pdb=" C04 X5M B2003 " pdb=" N03 X5M B2003 " ideal model delta sigma weight residual 115.49 104.75 10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C05 X5M C2003 " pdb=" C04 X5M C2003 " pdb=" N03 X5M C2003 " ideal model delta sigma weight residual 115.49 104.75 10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C PRO C 988 " pdb=" N PHE C 989 " pdb=" CA PHE C 989 " ideal model delta sigma weight residual 121.54 125.94 -4.40 1.91e+00 2.74e-01 5.31e+00 angle pdb=" C PRO B 988 " pdb=" N PHE B 989 " pdb=" CA PHE B 989 " ideal model delta sigma weight residual 121.54 125.94 -4.40 1.91e+00 2.74e-01 5.31e+00 angle pdb=" C07 X5M C2003 " pdb=" C06 X5M C2003 " pdb=" N03 X5M C2003 " ideal model delta sigma weight residual 122.57 116.98 5.59 3.00e+00 1.11e-01 3.47e+00 ... (remaining 8625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.15: 3487 11.15 - 22.31: 189 22.31 - 33.46: 52 33.46 - 44.61: 10 44.61 - 55.76: 4 Dihedral angle restraints: 3742 sinusoidal: 1512 harmonic: 2230 Sorted by residual: dihedral pdb=" CA MET C 835 " pdb=" C MET C 835 " pdb=" N HIS C 836 " pdb=" CA HIS C 836 " ideal model delta harmonic sigma weight residual -180.00 -166.06 -13.94 0 5.00e+00 4.00e-02 7.77e+00 dihedral pdb=" CA MET B 835 " pdb=" C MET B 835 " pdb=" N HIS B 836 " pdb=" CA HIS B 836 " ideal model delta harmonic sigma weight residual -180.00 -166.06 -13.94 0 5.00e+00 4.00e-02 7.77e+00 dihedral pdb=" N MET B 944 " pdb=" CA MET B 944 " pdb=" CB MET B 944 " pdb=" CG MET B 944 " ideal model delta sinusoidal sigma weight residual -60.00 -93.08 33.08 3 1.50e+01 4.44e-03 5.50e+00 ... (remaining 3739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 744 0.042 - 0.083: 154 0.083 - 0.125: 29 0.125 - 0.167: 3 0.167 - 0.208: 2 Chirality restraints: 932 Sorted by residual: chirality pdb=" C21 X5M C2003 " pdb=" C15 X5M C2003 " pdb=" C20 X5M C2003 " pdb=" C22 X5M C2003 " both_signs ideal model delta sigma weight residual False -2.63 -2.84 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C21 X5M B2003 " pdb=" C15 X5M B2003 " pdb=" C20 X5M B2003 " pdb=" C22 X5M B2003 " both_signs ideal model delta sigma weight residual False -2.63 -2.84 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE B 821 " pdb=" N ILE B 821 " pdb=" C ILE B 821 " pdb=" CB ILE B 821 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 929 not shown) Planarity restraints: 1114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 X5M B2003 " 0.057 2.00e-02 2.50e+03 1.00e-01 1.01e+02 pdb=" C04 X5M B2003 " 0.057 2.00e-02 2.50e+03 pdb=" C06 X5M B2003 " 0.060 2.00e-02 2.50e+03 pdb=" N03 X5M B2003 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 X5M C2003 " 0.057 2.00e-02 2.50e+03 1.00e-01 1.01e+02 pdb=" C04 X5M C2003 " 0.057 2.00e-02 2.50e+03 pdb=" C06 X5M C2003 " 0.060 2.00e-02 2.50e+03 pdb=" N03 X5M C2003 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 X5M C2003 " 0.014 2.00e-02 2.50e+03 5.86e-02 4.29e+01 pdb=" C20 X5M C2003 " 0.016 2.00e-02 2.50e+03 pdb=" N16 X5M C2003 " -0.069 2.00e-02 2.50e+03 pdb=" N17 X5M C2003 " 0.094 2.00e-02 2.50e+03 pdb=" O19 X5M C2003 " -0.055 2.00e-02 2.50e+03 ... (remaining 1111 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 28 2.42 - 3.04: 4030 3.04 - 3.66: 9259 3.66 - 4.28: 14464 4.28 - 4.90: 24145 Nonbonded interactions: 51926 Sorted by model distance: nonbonded pdb=" OD1 ASP B 950 " pdb="MN MN B2001 " model vdw 1.795 2.320 nonbonded pdb=" OD1 ASP C 950 " pdb="MN MN C2001 " model vdw 1.795 2.320 nonbonded pdb=" OD2 ASP B 837 " pdb="MN MN B2001 " model vdw 2.046 2.320 nonbonded pdb=" OD2 ASP C 837 " pdb="MN MN C2001 " model vdw 2.046 2.320 nonbonded pdb=" OD1 ASP C 837 " pdb="MG MG C2002 " model vdw 2.142 2.170 ... (remaining 51921 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'A' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.760 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 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 0.040 6358 Z= 0.120 Angle : 0.495 10.737 8630 Z= 0.262 Chirality : 0.036 0.208 932 Planarity : 0.006 0.100 1114 Dihedral : 7.938 55.764 2298 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.30 % Allowed : 1.81 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.31), residues: 746 helix: 2.83 (0.22), residues: 504 sheet: None (None), residues: 0 loop : 1.32 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 862 TYR 0.011 0.001 TYR C 738 PHE 0.009 0.001 PHE B 735 TRP 0.008 0.001 TRP C 874 HIS 0.002 0.000 HIS B 869 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 6358) covalent geometry : angle 0.49507 / 0.26 ( 8630) hydrogen bonds : bond 0.12858 / 8.24 ( 394) hydrogen bonds : angle 4.25953 / 3.08 ( 1116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.254 Fit side-chains REVERT: D 560 ILE cc_start: 0.7905 (mt) cc_final: 0.7703 (mt) outliers start: 2 outliers final: 2 residues processed: 72 average time/residue: 0.5592 time to fit residues: 42.3927 Evaluate side-chains 42 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 710 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3194 r_free = 0.3194 target = 0.045331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.037532 restraints weight = 32514.580| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 4.11 r_work: 0.2806 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6358 Z= 0.103 Angle : 0.476 7.206 8630 Z= 0.234 Chirality : 0.037 0.143 932 Planarity : 0.004 0.035 1114 Dihedral : 4.122 37.829 826 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.51 % Allowed : 6.63 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.57 (0.31), residues: 746 helix: 2.79 (0.22), residues: 512 sheet: None (None), residues: 0 loop : 1.55 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 862 TYR 0.009 0.001 TYR A 555 PHE 0.009 0.001 PHE B 897 TRP 0.007 0.001 TRP C 874 HIS 0.001 0.000 HIS C 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 6358) covalent geometry : angle 0.47610 / 0.23 ( 8630) hydrogen bonds : bond 0.03116 / 2.01 ( 394) hydrogen bonds : angle 3.48592 / 2.50 ( 1116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.236 Fit side-chains REVERT: B 802 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8707 (p) REVERT: B 1085 MET cc_start: 0.9289 (ttp) cc_final: 0.9072 (tmm) REVERT: C 802 VAL cc_start: 0.9086 (OUTLIER) cc_final: 0.8729 (p) REVERT: C 1085 MET cc_start: 0.9286 (ttp) cc_final: 0.9070 (tmm) outliers start: 10 outliers final: 2 residues processed: 52 average time/residue: 0.3601 time to fit residues: 20.3374 Evaluate side-chains 42 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 802 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 72 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 693 ASN B 999 ASN B1074 GLN C 999 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.044091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036521 restraints weight = 32293.676| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.93 r_work: 0.2785 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6358 Z= 0.109 Angle : 0.463 8.339 8630 Z= 0.227 Chirality : 0.036 0.133 932 Planarity : 0.004 0.035 1114 Dihedral : 4.004 32.850 826 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.81 % Allowed : 6.48 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.72 (0.30), residues: 746 helix: 2.94 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.49 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 862 TYR 0.010 0.001 TYR C 738 PHE 0.009 0.001 PHE B 897 TRP 0.009 0.001 TRP B1026 HIS 0.002 0.000 HIS C 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 6358) covalent geometry : angle 0.46286 / 0.23 ( 8630) hydrogen bonds : bond 0.02834 / 1.84 ( 394) hydrogen bonds : angle 3.36979 / 2.41 ( 1116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.223 Fit side-chains REVERT: B 736 MET cc_start: 0.9312 (mpp) cc_final: 0.8848 (mpp) REVERT: B 1085 MET cc_start: 0.9297 (ttp) cc_final: 0.9077 (tmm) REVERT: C 736 MET cc_start: 0.9312 (mpp) cc_final: 0.8849 (mpp) REVERT: C 944 MET cc_start: 0.9273 (tpp) cc_final: 0.9029 (mtp) REVERT: C 1085 MET cc_start: 0.9289 (ttp) cc_final: 0.9066 (tmm) outliers start: 12 outliers final: 3 residues processed: 49 average time/residue: 0.4053 time to fit residues: 21.3826 Evaluate side-chains 38 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain C residue 710 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 0 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 693 ASN C1074 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.043164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.035660 restraints weight = 32352.945| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.86 r_work: 0.2755 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6358 Z= 0.147 Angle : 0.488 7.760 8630 Z= 0.240 Chirality : 0.037 0.136 932 Planarity : 0.004 0.035 1114 Dihedral : 3.943 28.963 826 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.81 % Allowed : 7.08 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.80 (0.31), residues: 746 helix: 3.03 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.44 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 862 TYR 0.009 0.001 TYR B1016 PHE 0.008 0.001 PHE B 735 TRP 0.007 0.001 TRP C 932 HIS 0.003 0.001 HIS C 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 6358) covalent geometry : angle 0.48767 / 0.24 ( 8630) hydrogen bonds : bond 0.02924 / 1.89 ( 394) hydrogen bonds : angle 3.46419 / 2.48 ( 1116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.252 Fit side-chains REVERT: B 736 MET cc_start: 0.9322 (mpp) cc_final: 0.8797 (mpp) REVERT: B 738 TYR cc_start: 0.9408 (t80) cc_final: 0.9134 (t80) REVERT: B 878 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8094 (mpt) REVERT: B 990 MET cc_start: 0.9241 (mtm) cc_final: 0.8786 (mmm) REVERT: C 736 MET cc_start: 0.9326 (mpp) cc_final: 0.8799 (mpp) REVERT: C 738 TYR cc_start: 0.9407 (t80) cc_final: 0.9140 (t80) REVERT: C 878 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8086 (mpt) REVERT: C 990 MET cc_start: 0.9236 (mtm) cc_final: 0.8170 (mmm) outliers start: 12 outliers final: 2 residues processed: 46 average time/residue: 0.3910 time to fit residues: 19.2194 Evaluate side-chains 39 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 878 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 65 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3122 r_free = 0.3122 target = 0.042189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.034630 restraints weight = 32836.676| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.98 r_work: 0.2720 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6358 Z= 0.204 Angle : 0.525 8.085 8630 Z= 0.262 Chirality : 0.039 0.134 932 Planarity : 0.004 0.036 1114 Dihedral : 4.024 26.684 826 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.36 % Allowed : 7.68 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.69 (0.31), residues: 746 helix: 2.93 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.46 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 717 TYR 0.011 0.001 TYR B1016 PHE 0.010 0.001 PHE B 735 TRP 0.006 0.001 TRP C 932 HIS 0.004 0.001 HIS C 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 ( 6358) covalent geometry : angle 0.52515 / 0.26 ( 8630) hydrogen bonds : bond 0.03289 / 2.12 ( 394) hydrogen bonds : angle 3.59288 / 2.57 ( 1116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: B 736 MET cc_start: 0.9351 (mpp) cc_final: 0.8884 (mpp) REVERT: B 738 TYR cc_start: 0.9458 (t80) cc_final: 0.9165 (t80) REVERT: B 878 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8080 (mpt) REVERT: C 736 MET cc_start: 0.9343 (mpp) cc_final: 0.8871 (mpp) REVERT: C 738 TYR cc_start: 0.9459 (t80) cc_final: 0.9153 (t80) REVERT: C 878 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8059 (mpt) REVERT: C 990 MET cc_start: 0.9247 (mtm) cc_final: 0.8369 (mmm) outliers start: 9 outliers final: 2 residues processed: 41 average time/residue: 0.3937 time to fit residues: 17.3508 Evaluate side-chains 37 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 878 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 48 optimal weight: 6.9990 chunk 68 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3171 r_free = 0.3171 target = 0.043697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.036200 restraints weight = 32284.352| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.03 r_work: 0.2776 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6358 Z= 0.103 Angle : 0.481 9.331 8630 Z= 0.232 Chirality : 0.037 0.135 932 Planarity : 0.004 0.036 1114 Dihedral : 3.827 27.975 826 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.05 % Allowed : 8.13 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.76 (0.31), residues: 746 helix: 2.98 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.48 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 862 TYR 0.007 0.001 TYR C1016 PHE 0.008 0.001 PHE B 897 TRP 0.006 0.001 TRP C 932 HIS 0.002 0.000 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 ( 6358) covalent geometry : angle 0.48126 / 0.23 ( 8630) hydrogen bonds : bond 0.02753 / 1.80 ( 394) hydrogen bonds : angle 3.36480 / 2.40 ( 1116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.178 Fit side-chains REVERT: B 736 MET cc_start: 0.9332 (mpp) cc_final: 0.8778 (mpp) REVERT: B 738 TYR cc_start: 0.9437 (t80) cc_final: 0.9128 (t80) REVERT: B 878 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8096 (mpt) REVERT: B 903 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8912 (tp30) REVERT: C 736 MET cc_start: 0.9339 (mpp) cc_final: 0.8788 (mpp) REVERT: C 738 TYR cc_start: 0.9420 (t80) cc_final: 0.9102 (t80) REVERT: C 759 ASP cc_start: 0.9424 (t70) cc_final: 0.9167 (OUTLIER) REVERT: C 878 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8072 (mpt) REVERT: C 903 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8926 (tp30) outliers start: 7 outliers final: 3 residues processed: 40 average time/residue: 0.4015 time to fit residues: 17.1227 Evaluate side-chains 39 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 878 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 0.0370 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 = 0.3175 r_free = 0.3175 target = 0.043856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.036350 restraints weight = 32350.347| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 4.06 r_work: 0.2784 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6358 Z= 0.104 Angle : 0.491 10.153 8630 Z= 0.234 Chirality : 0.036 0.134 932 Planarity : 0.004 0.035 1114 Dihedral : 3.756 26.568 826 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.20 % Allowed : 8.58 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.80 (0.31), residues: 746 helix: 3.00 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.52 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 862 TYR 0.007 0.001 TYR B1016 PHE 0.008 0.001 PHE B 735 TRP 0.006 0.001 TRP C 932 HIS 0.002 0.000 HIS C1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 ( 6358) covalent geometry : angle 0.49055 / 0.23 ( 8630) hydrogen bonds : bond 0.02690 / 1.75 ( 394) hydrogen bonds : angle 3.34363 / 2.38 ( 1116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 736 MET cc_start: 0.9343 (tpp) cc_final: 0.8807 (mpp) REVERT: B 738 TYR cc_start: 0.9446 (t80) cc_final: 0.9130 (t80) REVERT: B 759 ASP cc_start: 0.9361 (t70) cc_final: 0.9081 (OUTLIER) REVERT: B 903 GLU cc_start: 0.9311 (mm-30) cc_final: 0.8909 (tp30) REVERT: C 736 MET cc_start: 0.9348 (tpp) cc_final: 0.8813 (mpp) REVERT: C 738 TYR cc_start: 0.9438 (t80) cc_final: 0.9098 (t80) REVERT: C 759 ASP cc_start: 0.9418 (t70) cc_final: 0.9161 (OUTLIER) REVERT: C 903 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8878 (tp30) outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 0.3844 time to fit residues: 16.8908 Evaluate side-chains 40 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 990 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 990 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.044030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036601 restraints weight = 31978.275| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 4.03 r_work: 0.2790 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6358 Z= 0.104 Angle : 0.544 11.246 8630 Z= 0.250 Chirality : 0.037 0.134 932 Planarity : 0.004 0.036 1114 Dihedral : 3.709 25.836 826 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.90 % Allowed : 8.73 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.84 (0.31), residues: 746 helix: 3.02 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.55 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 862 TYR 0.008 0.001 TYR C1016 PHE 0.008 0.001 PHE B 735 TRP 0.007 0.001 TRP B 874 HIS 0.002 0.000 HIS C 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 ( 6358) covalent geometry : angle 0.54401 / 0.25 ( 8630) hydrogen bonds : bond 0.02679 / 1.75 ( 394) hydrogen bonds : angle 3.34407 / 2.38 ( 1116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: B 736 MET cc_start: 0.9346 (tpp) cc_final: 0.8815 (mpp) REVERT: B 738 TYR cc_start: 0.9433 (t80) cc_final: 0.9083 (t80) REVERT: B 759 ASP cc_start: 0.9357 (t70) cc_final: 0.9084 (OUTLIER) REVERT: B 903 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8914 (tp30) REVERT: C 736 MET cc_start: 0.9340 (tpp) cc_final: 0.8803 (mpp) REVERT: C 738 TYR cc_start: 0.9436 (t80) cc_final: 0.9071 (t80) REVERT: C 759 ASP cc_start: 0.9403 (t70) cc_final: 0.9154 (OUTLIER) REVERT: C 903 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8849 (tp30) REVERT: C 944 MET cc_start: 0.8808 (mtm) cc_final: 0.8490 (mtm) REVERT: C 990 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8870 (mmm) outliers start: 6 outliers final: 5 residues processed: 43 average time/residue: 0.4416 time to fit residues: 20.3224 Evaluate side-chains 40 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 990 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 990 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 23 optimal weight: 0.0070 chunk 54 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- 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 = 0.3191 r_free = 0.3191 target = 0.044369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.036759 restraints weight = 31931.155| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 4.05 r_work: 0.2792 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6358 Z= 0.100 Angle : 0.535 11.946 8630 Z= 0.250 Chirality : 0.037 0.148 932 Planarity : 0.004 0.035 1114 Dihedral : 3.718 25.289 826 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.90 % Allowed : 9.19 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.82 (0.31), residues: 746 helix: 3.01 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.55 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 862 TYR 0.011 0.001 TYR C 830 PHE 0.061 0.001 PHE C 920 TRP 0.009 0.001 TRP B1086 HIS 0.002 0.000 HIS C1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 6358) covalent geometry : angle 0.53462 / 0.25 ( 8630) hydrogen bonds : bond 0.02654 / 1.74 ( 394) hydrogen bonds : angle 3.37188 / 2.41 ( 1116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: B 736 MET cc_start: 0.9353 (tpp) cc_final: 0.8790 (mpp) REVERT: B 738 TYR cc_start: 0.9433 (t80) cc_final: 0.9098 (t80) REVERT: B 759 ASP cc_start: 0.9338 (t70) cc_final: 0.9071 (OUTLIER) REVERT: B 903 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8894 (tp30) REVERT: B 1085 MET cc_start: 0.9310 (ttp) cc_final: 0.8942 (pp-130) REVERT: C 736 MET cc_start: 0.9355 (tpp) cc_final: 0.8790 (mpp) REVERT: C 738 TYR cc_start: 0.9414 (t80) cc_final: 0.9070 (t80) REVERT: C 759 ASP cc_start: 0.9383 (t70) cc_final: 0.9138 (OUTLIER) REVERT: C 903 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8830 (tp30) REVERT: C 990 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.8982 (mmm) REVERT: C 1085 MET cc_start: 0.9316 (ttp) cc_final: 0.8955 (pp-130) outliers start: 6 outliers final: 5 residues processed: 42 average time/residue: 0.4585 time to fit residues: 20.5513 Evaluate side-chains 42 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 990 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 990 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 16 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 740 HIS C 740 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.044636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.037174 restraints weight = 32162.094| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.04 r_work: 0.2810 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6358 Z= 0.099 Angle : 0.577 13.475 8630 Z= 0.264 Chirality : 0.037 0.162 932 Planarity : 0.004 0.035 1114 Dihedral : 3.686 24.959 826 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.60 % Allowed : 9.34 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.72 (0.31), residues: 746 helix: 2.93 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.53 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 862 TYR 0.007 0.001 TYR C1016 PHE 0.026 0.001 PHE C 920 TRP 0.010 0.001 TRP B 874 HIS 0.002 0.000 HIS C 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 6358) covalent geometry : angle 0.57661 / 0.26 ( 8630) hydrogen bonds : bond 0.02645 / 1.71 ( 394) hydrogen bonds : angle 3.42453 / 2.45 ( 1116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: B 736 MET cc_start: 0.9347 (tpp) cc_final: 0.8796 (mpp) REVERT: B 738 TYR cc_start: 0.9438 (t80) cc_final: 0.9089 (t80) REVERT: B 759 ASP cc_start: 0.9331 (t70) cc_final: 0.9056 (OUTLIER) REVERT: B 903 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8929 (tp30) REVERT: B 1085 MET cc_start: 0.9288 (ttp) cc_final: 0.8942 (pp-130) REVERT: C 736 MET cc_start: 0.9342 (tpp) cc_final: 0.8799 (mpp) REVERT: C 738 TYR cc_start: 0.9413 (t80) cc_final: 0.8997 (t80) REVERT: C 759 ASP cc_start: 0.9398 (t70) cc_final: 0.9140 (OUTLIER) REVERT: C 903 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8887 (tp30) REVERT: C 990 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8935 (mmm) REVERT: C 1085 MET cc_start: 0.9294 (ttp) cc_final: 0.8945 (pp-130) outliers start: 4 outliers final: 5 residues processed: 41 average time/residue: 0.4215 time to fit residues: 18.5194 Evaluate side-chains 42 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 990 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 990 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 54 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.0470 chunk 68 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.045063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.037601 restraints weight = 31871.862| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 4.02 r_work: 0.2822 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6358 Z= 0.096 Angle : 0.586 13.064 8630 Z= 0.263 Chirality : 0.037 0.136 932 Planarity : 0.004 0.035 1114 Dihedral : 3.640 24.701 826 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.75 % Allowed : 9.79 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.77 (0.31), residues: 746 helix: 2.98 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.50 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 862 TYR 0.013 0.001 TYR C 830 PHE 0.043 0.001 PHE C 920 TRP 0.006 0.001 TRP B 932 HIS 0.001 0.000 HIS C1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 6358) covalent geometry : angle 0.58574 / 0.26 ( 8630) hydrogen bonds : bond 0.02594 / 1.68 ( 394) hydrogen bonds : angle 3.36689 / 2.40 ( 1116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1545.26 seconds wall clock time: 27 minutes 14.63 seconds (1634.63 seconds total)