Starting phenix.real_space_refine on Tue Mar 3 14:51:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lrc_23494/03_2026/7lrc_23494.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lrc_23494/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7lrc_23494/03_2026/7lrc_23494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lrc_23494/03_2026/7lrc_23494.map" model { file = "/net/cci-nas-00/data/ceres_data/7lrc_23494/03_2026/7lrc_23494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lrc_23494/03_2026/7lrc_23494.cif" } 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-5986/lib/python3.9/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: 2.00, per 1000 atoms: 0.32 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: 0.61 Conformation dependent library (CDL) restraints added in 282.9 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: 0.19 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: 0.95 Time building geometry restraints manager: 0.73 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: 3503 11.15 - 22.31: 189 22.31 - 33.46: 52 33.46 - 44.61: 14 44.61 - 55.76: 4 Dihedral angle restraints: 3762 sinusoidal: 1532 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 3759 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: 2.440 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: 0.030 Set scattering table: 0.010 Process input model: 8.090 Find NCS groups from input model: 0.050 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 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 : 8.071 55.764 2318 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 covalent geometry : bond 0.00240 ( 6358) covalent geometry : angle 0.49507 ( 8630) hydrogen bonds : bond 0.12858 ( 394) hydrogen bonds : angle 4.25953 ( 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 : 0.260 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: 0.6231 time to fit residues: 47.0398 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 : 0.255 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.045304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.037523 restraints weight = 32540.242| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 4.10 r_work: 0.2805 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6358 Z= 0.105 Angle : 0.478 7.326 8630 Z= 0.236 Chirality : 0.037 0.140 932 Planarity : 0.004 0.035 1114 Dihedral : 4.518 40.443 846 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.96 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 : 1.54 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 covalent geometry : bond 0.00232 ( 6358) covalent geometry : angle 0.47845 ( 8630) hydrogen bonds : bond 0.03071 ( 394) hydrogen bonds : angle 3.49456 ( 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 51 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.237 Fit side-chains REVERT: B 802 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8717 (p) REVERT: B 1085 MET cc_start: 0.9287 (ttp) cc_final: 0.9074 (tmm) REVERT: C 802 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8740 (p) REVERT: C 1085 MET cc_start: 0.9284 (ttp) cc_final: 0.9073 (tmm) outliers start: 10 outliers final: 2 residues processed: 51 average time/residue: 0.4102 time to fit residues: 22.5450 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 : 0.233 ------------------------------------------------------------------------------- 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: 0.3980 chunk 6 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 30 optimal weight: 0.0470 chunk 54 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1074 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.044641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.036934 restraints weight = 32404.547| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.99 r_work: 0.2802 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1777 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= 0.094 Angle : 0.460 8.795 8630 Z= 0.224 Chirality : 0.036 0.142 932 Planarity : 0.004 0.034 1114 Dihedral : 4.475 39.165 846 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.11 % Allowed : 6.17 % 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: 3.71 (0.30), residues: 746 helix: 2.92 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.52 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 862 TYR 0.009 0.001 TYR B 738 PHE 0.010 0.001 PHE B 897 TRP 0.007 0.001 TRP C 874 HIS 0.002 0.000 HIS C 868 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 6358) covalent geometry : angle 0.46049 ( 8630) hydrogen bonds : bond 0.02704 ( 394) hydrogen bonds : angle 3.38696 ( 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 57 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.243 Fit side-chains REVERT: B 736 MET cc_start: 0.9316 (mpp) cc_final: 0.8873 (mpp) REVERT: B 1085 MET cc_start: 0.9282 (ttp) cc_final: 0.9044 (tmm) REVERT: C 736 MET cc_start: 0.9316 (mpp) cc_final: 0.8863 (mpp) REVERT: C 944 MET cc_start: 0.9282 (tpp) cc_final: 0.9067 (mtp) REVERT: C 1085 MET cc_start: 0.9276 (ttp) cc_final: 0.9038 (tmm) outliers start: 14 outliers final: 2 residues processed: 53 average time/residue: 0.3513 time to fit residues: 20.1580 Evaluate side-chains 39 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 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: 3.9990 chunk 55 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 693 ASN B1074 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.044040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.036383 restraints weight = 32382.234| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 4.01 r_work: 0.2779 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6358 Z= 0.115 Angle : 0.467 7.790 8630 Z= 0.229 Chirality : 0.037 0.133 932 Planarity : 0.004 0.035 1114 Dihedral : 4.472 40.715 846 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.36 % Allowed : 7.08 % Favored : 91.57 % 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: 3.78 (0.30), residues: 746 helix: 3.01 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.44 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 862 TYR 0.014 0.001 TYR B 738 PHE 0.009 0.001 PHE B 739 TRP 0.008 0.001 TRP C1026 HIS 0.002 0.001 HIS C 868 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6358) covalent geometry : angle 0.46671 ( 8630) hydrogen bonds : bond 0.02753 ( 394) hydrogen bonds : angle 3.37075 ( 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 48 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.257 Fit side-chains REVERT: B 736 MET cc_start: 0.9312 (mpp) cc_final: 0.8836 (mpp) REVERT: B 878 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8232 (mpt) REVERT: B 990 MET cc_start: 0.9265 (mtm) cc_final: 0.8077 (mmm) REVERT: B 1085 MET cc_start: 0.9273 (ttp) cc_final: 0.9049 (tmm) REVERT: C 736 MET cc_start: 0.9324 (mpp) cc_final: 0.8853 (mpp) REVERT: C 878 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8219 (mpt) REVERT: C 990 MET cc_start: 0.9256 (mtm) cc_final: 0.8073 (mmm) REVERT: C 1085 MET cc_start: 0.9266 (ttp) cc_final: 0.9039 (tmm) outliers start: 9 outliers final: 2 residues processed: 45 average time/residue: 0.5016 time to fit residues: 24.0444 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 : 0.235 ------------------------------------------------------------------------------- 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: 5.9990 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 70 optimal weight: 0.0370 chunk 34 optimal weight: 3.9990 overall best weight: 2.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 999 ASN C 999 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.041922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.034457 restraints weight = 32504.257| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.93 r_work: 0.2710 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 6358 Z= 0.254 Angle : 0.568 7.638 8630 Z= 0.285 Chirality : 0.040 0.135 932 Planarity : 0.004 0.036 1114 Dihedral : 4.667 41.989 846 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.66 % Allowed : 7.38 % 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: 3.55 (0.31), residues: 746 helix: 2.82 (0.22), residues: 516 sheet: None (None), residues: 0 loop : 1.38 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 717 TYR 0.013 0.002 TYR C 738 PHE 0.010 0.002 PHE C 735 TRP 0.008 0.001 TRP C1026 HIS 0.004 0.001 HIS C 868 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 6358) covalent geometry : angle 0.56794 ( 8630) hydrogen bonds : bond 0.03556 ( 394) hydrogen bonds : angle 3.72807 ( 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 45 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.217 Fit side-chains REVERT: B 736 MET cc_start: 0.9353 (mpp) cc_final: 0.8885 (mpp) REVERT: B 878 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8028 (mpt) REVERT: B 903 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8910 (tp30) REVERT: B 990 MET cc_start: 0.9295 (mtm) cc_final: 0.8469 (mmm) REVERT: C 736 MET cc_start: 0.9356 (mpp) cc_final: 0.8887 (mpp) REVERT: C 878 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8011 (mpt) REVERT: C 990 MET cc_start: 0.9281 (mtm) cc_final: 0.8460 (mmm) outliers start: 11 outliers final: 2 residues processed: 43 average time/residue: 0.4516 time to fit residues: 20.8328 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 : 0.243 ------------------------------------------------------------------------------- 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: 2.9990 chunk 68 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3161 r_free = 0.3161 target = 0.043401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.035955 restraints weight = 32019.525| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.95 r_work: 0.2767 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2513 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= 0.111 Angle : 0.486 9.343 8630 Z= 0.236 Chirality : 0.037 0.142 932 Planarity : 0.004 0.036 1114 Dihedral : 4.450 41.795 846 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.20 % Allowed : 7.38 % Favored : 91.42 % 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: 2.98 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.37 (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 B1026 HIS 0.002 0.000 HIS B 868 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6358) covalent geometry : angle 0.48605 ( 8630) hydrogen bonds : bond 0.02888 ( 394) hydrogen bonds : angle 3.38717 ( 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 42 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.268 Fit side-chains REVERT: B 736 MET cc_start: 0.9337 (mpp) cc_final: 0.8815 (mpp) REVERT: B 878 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.7973 (mpt) REVERT: B 903 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8912 (tp30) REVERT: C 736 MET cc_start: 0.9344 (mpp) cc_final: 0.8820 (mpp) REVERT: C 878 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.7966 (mpt) REVERT: C 903 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8909 (tp30) outliers start: 8 outliers final: 2 residues processed: 39 average time/residue: 0.5223 time to fit residues: 21.7351 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 : 0.244 ------------------------------------------------------------------------------- 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: 6.9990 chunk 70 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3166 r_free = 0.3166 target = 0.043606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.036184 restraints weight = 32216.226| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.98 r_work: 0.2777 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6358 Z= 0.110 Angle : 0.487 10.184 8630 Z= 0.234 Chirality : 0.037 0.138 932 Planarity : 0.004 0.036 1114 Dihedral : 4.390 42.394 846 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.20 % Allowed : 8.13 % Favored : 90.66 % 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: 3.71 (0.31), residues: 746 helix: 2.96 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.40 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 862 TYR 0.011 0.001 TYR B 738 PHE 0.009 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 covalent geometry : bond 0.00259 ( 6358) covalent geometry : angle 0.48680 ( 8630) hydrogen bonds : bond 0.02808 ( 394) hydrogen bonds : angle 3.36047 ( 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 46 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 736 MET cc_start: 0.9355 (mpp) cc_final: 0.8824 (mpp) REVERT: B 759 ASP cc_start: 0.9395 (t70) cc_final: 0.9115 (OUTLIER) REVERT: B 878 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.7995 (mpt) REVERT: B 903 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8888 (tp30) REVERT: B 1085 MET cc_start: 0.9275 (ttp) cc_final: 0.8767 (pp-130) REVERT: C 736 MET cc_start: 0.9350 (mpp) cc_final: 0.8816 (mpp) REVERT: C 759 ASP cc_start: 0.9397 (t70) cc_final: 0.9117 (OUTLIER) REVERT: C 878 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.7996 (mpt) REVERT: C 903 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8845 (tp30) REVERT: C 1085 MET cc_start: 0.9328 (ttp) cc_final: 0.8876 (pp-130) outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 0.5053 time to fit residues: 22.6483 Evaluate side-chains 43 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain B residue 990 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 878 MET 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: 0.9990 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.3165 r_free = 0.3165 target = 0.043516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.036020 restraints weight = 31921.081| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 4.01 r_work: 0.2769 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6358 Z= 0.122 Angle : 0.526 11.221 8630 Z= 0.248 Chirality : 0.037 0.135 932 Planarity : 0.004 0.036 1114 Dihedral : 4.397 42.589 846 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.20 % Allowed : 9.19 % Favored : 89.61 % 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: 3.79 (0.31), residues: 746 helix: 2.92 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.71 (0.45), 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 C 735 TRP 0.006 0.001 TRP C 932 HIS 0.002 0.001 HIS B 868 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6358) covalent geometry : angle 0.52635 ( 8630) hydrogen bonds : bond 0.02839 ( 394) hydrogen bonds : angle 3.40301 ( 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 46 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: B 736 MET cc_start: 0.9351 (tpp) cc_final: 0.8824 (mpp) REVERT: B 738 TYR cc_start: 0.9411 (t80) cc_final: 0.9131 (t80) REVERT: B 759 ASP cc_start: 0.9388 (t70) cc_final: 0.9122 (OUTLIER) REVERT: B 878 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.7967 (mpt) REVERT: B 903 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8864 (tp30) REVERT: B 1085 MET cc_start: 0.9305 (ttp) cc_final: 0.9054 (tmm) REVERT: C 736 MET cc_start: 0.9358 (tpp) cc_final: 0.8823 (mpp) REVERT: C 759 ASP cc_start: 0.9410 (t70) cc_final: 0.9151 (OUTLIER) REVERT: C 878 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.7997 (mpt) REVERT: C 903 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8827 (tp30) REVERT: C 944 MET cc_start: 0.8891 (mtm) cc_final: 0.8650 (mtm) REVERT: C 990 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.8930 (mmm) REVERT: C 1085 MET cc_start: 0.9302 (ttp) cc_final: 0.9087 (tmm) outliers start: 8 outliers final: 7 residues processed: 42 average time/residue: 0.4790 time to fit residues: 21.5442 Evaluate side-chains 46 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain B residue 990 MET Chi-restraints excluded: chain B residue 1090 ILE Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 990 MET Chi-restraints excluded: chain C residue 1090 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 72 optimal weight: 0.0980 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.043846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.036431 restraints weight = 31994.428| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 4.00 r_work: 0.2785 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6358 Z= 0.107 Angle : 0.538 12.957 8630 Z= 0.248 Chirality : 0.037 0.138 932 Planarity : 0.004 0.036 1114 Dihedral : 4.375 42.720 846 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.20 % Allowed : 9.04 % Favored : 89.76 % 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: 3.86 (0.31), residues: 746 helix: 2.98 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.72 (0.45), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 862 TYR 0.010 0.001 TYR C 738 PHE 0.008 0.001 PHE C 735 TRP 0.006 0.001 TRP C1026 HIS 0.002 0.000 HIS C 868 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6358) covalent geometry : angle 0.53761 ( 8630) hydrogen bonds : bond 0.02732 ( 394) hydrogen bonds : angle 3.36392 ( 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 46 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: B 736 MET cc_start: 0.9356 (tpp) cc_final: 0.8837 (mpp) REVERT: B 738 TYR cc_start: 0.9427 (t80) cc_final: 0.9115 (t80) REVERT: B 759 ASP cc_start: 0.9380 (t70) cc_final: 0.9102 (OUTLIER) REVERT: B 903 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8871 (tp30) REVERT: B 1085 MET cc_start: 0.9304 (ttp) cc_final: 0.9054 (tmm) REVERT: C 736 MET cc_start: 0.9349 (tpp) cc_final: 0.8800 (mpp) REVERT: C 759 ASP cc_start: 0.9404 (t70) cc_final: 0.9132 (OUTLIER) REVERT: C 835 MET cc_start: 0.9255 (ptp) cc_final: 0.8798 (pmm) REVERT: C 903 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8821 (tp30) REVERT: C 990 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.8995 (mmm) REVERT: C 1085 MET cc_start: 0.9297 (ttp) cc_final: 0.9081 (tmm) outliers start: 8 outliers final: 7 residues processed: 42 average time/residue: 0.4840 time to fit residues: 21.7045 Evaluate side-chains 44 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 990 MET Chi-restraints excluded: chain B residue 1090 ILE Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 990 MET Chi-restraints excluded: chain C residue 1090 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.0670 chunk 66 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 740 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.044255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.036715 restraints weight = 32060.551| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 4.03 r_work: 0.2794 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 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 : 0.002 0.033 6358 Z= 0.102 Angle : 0.539 13.039 8630 Z= 0.251 Chirality : 0.037 0.137 932 Planarity : 0.004 0.036 1114 Dihedral : 4.368 43.058 846 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.90 % Allowed : 9.04 % 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: 3.71 (0.31), residues: 746 helix: 2.94 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.46 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 862 TYR 0.013 0.001 TYR C1016 PHE 0.013 0.001 PHE C 920 TRP 0.009 0.001 TRP B 874 HIS 0.002 0.000 HIS B 836 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 6358) covalent geometry : angle 0.53915 ( 8630) hydrogen bonds : bond 0.02717 ( 394) hydrogen bonds : angle 3.39013 ( 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 45 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 736 MET cc_start: 0.9343 (tpp) cc_final: 0.8790 (mpp) REVERT: B 738 TYR cc_start: 0.9419 (t80) cc_final: 0.9026 (t80) REVERT: B 759 ASP cc_start: 0.9359 (t70) cc_final: 0.9082 (OUTLIER) REVERT: B 903 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8866 (tp30) REVERT: B 1085 MET cc_start: 0.9301 (ttp) cc_final: 0.9078 (tmm) REVERT: C 736 MET cc_start: 0.9347 (tpp) cc_final: 0.8801 (mpp) REVERT: C 759 ASP cc_start: 0.9379 (t70) cc_final: 0.9104 (OUTLIER) REVERT: C 835 MET cc_start: 0.9248 (ptp) cc_final: 0.8779 (pmm) REVERT: C 903 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8829 (tp30) outliers start: 6 outliers final: 8 residues processed: 43 average time/residue: 0.4867 time to fit residues: 22.4783 Evaluate side-chains 44 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 990 MET Chi-restraints excluded: chain B residue 1090 ILE Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 990 MET Chi-restraints excluded: chain C residue 1090 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 54 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3190 r_free = 0.3190 target = 0.044373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.036923 restraints weight = 31710.091| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 4.01 r_work: 0.2803 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6358 Z= 0.097 Angle : 0.552 13.456 8630 Z= 0.254 Chirality : 0.037 0.139 932 Planarity : 0.004 0.036 1114 Dihedral : 4.323 43.089 846 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.90 % Allowed : 9.49 % Favored : 89.61 % 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: 3.78 (0.31), residues: 746 helix: 2.99 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.49 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 862 TYR 0.008 0.001 TYR B1016 PHE 0.008 0.001 PHE C 739 TRP 0.009 0.001 TRP C 874 HIS 0.002 0.000 HIS B 836 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 6358) covalent geometry : angle 0.55194 ( 8630) hydrogen bonds : bond 0.02635 ( 394) hydrogen bonds : angle 3.37865 ( 1116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1701.71 seconds wall clock time: 29 minutes 55.88 seconds (1795.88 seconds total)