Starting phenix.real_space_refine on Tue Feb 11 17:09:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lrc_23494/02_2025/7lrc_23494.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lrc_23494/02_2025/7lrc_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_23494/02_2025/7lrc_23494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lrc_23494/02_2025/7lrc_23494.map" model { file = "/net/cci-nas-00/data/ceres_data/7lrc_23494/02_2025/7lrc_23494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lrc_23494/02_2025/7lrc_23494.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6202 Number of models: 1 Model: "" Number of chains: 3 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: "C" 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: "C" 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: B, D Time building chain proxies: 5.32, per 1000 atoms: 0.86 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: 1.55 Conformation dependent library (CDL) restraints added in 899.9 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: 0.52 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: 1.52 Time building geometry restraints manager: 1.73 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: 0.02 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'B' } 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: 1.670 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.430 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.180 ------------------------------------------------------------------------------- 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= 0.147 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 : 5.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP C 874 HIS 0.002 0.000 HIS B 869 PHE 0.009 0.001 PHE B 735 TYR 0.011 0.001 TYR C 738 ARG 0.001 0.000 ARG B 862 *********************** 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 : 0.745 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: 1.2529 time to fit residues: 94.9654 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 : 0.657 ------------------------------------------------------------------------------- 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 64 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 0.0770 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.045264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.037521 restraints weight = 31790.352| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 4.04 r_work: 0.2808 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1463 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= 0.143 Angle : 0.480 7.445 8630 Z= 0.236 Chirality : 0.037 0.136 932 Planarity : 0.004 0.035 1114 Dihedral : 4.536 40.664 846 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.31), residues: 746 helix: 2.78 (0.22), residues: 512 sheet: None (None), residues: 0 loop : 1.54 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 874 HIS 0.001 0.000 HIS C 868 PHE 0.009 0.001 PHE B 897 TYR 0.009 0.001 TYR A 555 ARG 0.004 0.000 ARG C 862 *********************** 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 53 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.758 Fit side-chains REVERT: B 802 VAL cc_start: 0.9090 (OUTLIER) cc_final: 0.8755 (p) REVERT: B 1085 MET cc_start: 0.9294 (ttp) cc_final: 0.9079 (tmm) REVERT: C 802 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8774 (p) REVERT: C 1085 MET cc_start: 0.9292 (ttp) cc_final: 0.9078 (tmm) outliers start: 10 outliers final: 2 residues processed: 53 average time/residue: 0.8946 time to fit residues: 51.6246 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 : 1.004 ------------------------------------------------------------------------------- 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: 5.9990 chunk 35 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.3136 r_free = 0.3136 target = 0.042632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.035198 restraints weight = 32856.212| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.84 r_work: 0.2735 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6358 Z= 0.248 Angle : 0.505 7.891 8630 Z= 0.252 Chirality : 0.038 0.137 932 Planarity : 0.004 0.035 1114 Dihedral : 4.592 41.302 846 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.66 % Allowed : 6.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.75 (0.31), residues: 746 helix: 3.02 (0.22), residues: 510 sheet: None (None), residues: 0 loop : 1.38 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1026 HIS 0.004 0.001 HIS B 868 PHE 0.009 0.001 PHE B 739 TYR 0.011 0.001 TYR B1016 ARG 0.003 0.001 ARG C 862 *********************** 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 51 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.677 Fit side-chains REVERT: B 736 MET cc_start: 0.9330 (mpp) cc_final: 0.8806 (mpp) REVERT: B 802 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8857 (p) REVERT: B 990 MET cc_start: 0.9236 (mtm) cc_final: 0.8837 (mmm) REVERT: C 736 MET cc_start: 0.9327 (mpp) cc_final: 0.8803 (mpp) REVERT: C 802 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8832 (p) outliers start: 11 outliers final: 2 residues processed: 49 average time/residue: 1.0583 time to fit residues: 55.6313 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 : 0.756 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 16 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3140 r_free = 0.3140 target = 0.042765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.035153 restraints weight = 33148.240| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.97 r_work: 0.2736 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2266 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= 0.216 Angle : 0.485 8.216 8630 Z= 0.241 Chirality : 0.037 0.130 932 Planarity : 0.004 0.036 1114 Dihedral : 4.509 42.360 846 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.66 % Allowed : 7.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.31), residues: 746 helix: 3.01 (0.23), residues: 510 sheet: None (None), residues: 0 loop : 1.46 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 932 HIS 0.003 0.001 HIS C 868 PHE 0.009 0.001 PHE B 735 TYR 0.009 0.001 TYR B1016 ARG 0.002 0.000 ARG C 862 *********************** 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: 11 poor density : 37 time to evaluate : 0.650 Fit side-chains REVERT: B 736 MET cc_start: 0.9328 (mpp) cc_final: 0.8801 (mpp) REVERT: B 738 TYR cc_start: 0.9437 (t80) cc_final: 0.9135 (t80) REVERT: B 759 ASP cc_start: 0.9448 (t70) cc_final: 0.9170 (OUTLIER) REVERT: B 878 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8078 (mpt) REVERT: B 903 GLU cc_start: 0.9304 (mm-30) cc_final: 0.9097 (mm-30) REVERT: B 1085 MET cc_start: 0.9347 (ttp) cc_final: 0.9090 (tmm) REVERT: C 736 MET cc_start: 0.9330 (mpp) cc_final: 0.8804 (mpp) REVERT: C 738 TYR cc_start: 0.9444 (t80) cc_final: 0.9147 (t80) REVERT: C 759 ASP cc_start: 0.9471 (t70) cc_final: 0.9180 (OUTLIER) REVERT: C 878 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8076 (mpt) REVERT: C 903 GLU cc_start: 0.9313 (mm-30) cc_final: 0.9020 (mm-30) REVERT: C 990 MET cc_start: 0.9265 (mtm) cc_final: 0.8322 (mmm) REVERT: C 1085 MET cc_start: 0.9341 (ttp) cc_final: 0.9081 (tmm) outliers start: 11 outliers final: 4 residues processed: 45 average time/residue: 0.9706 time to fit residues: 47.1024 Evaluate side-chains 41 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 14 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 23 optimal weight: 0.0870 chunk 16 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.3182 r_free = 0.3182 target = 0.044006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.036460 restraints weight = 32258.971| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.96 r_work: 0.2792 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6358 Z= 0.117 Angle : 0.456 8.648 8630 Z= 0.222 Chirality : 0.036 0.137 932 Planarity : 0.004 0.035 1114 Dihedral : 4.352 42.760 846 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.05 % Allowed : 7.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.31), residues: 746 helix: 3.03 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.48 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 932 HIS 0.002 0.000 HIS C1007 PHE 0.009 0.001 PHE C 897 TYR 0.007 0.001 TYR C1016 ARG 0.002 0.000 ARG C 862 *********************** 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 47 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: B 736 MET cc_start: 0.9294 (mpp) cc_final: 0.8733 (mpp) REVERT: B 738 TYR cc_start: 0.9414 (t80) cc_final: 0.9074 (t80) REVERT: B 759 ASP cc_start: 0.9418 (t70) cc_final: 0.9137 (OUTLIER) REVERT: B 903 GLU cc_start: 0.9319 (mm-30) cc_final: 0.9010 (mm-30) REVERT: B 1085 MET cc_start: 0.9349 (ttp) cc_final: 0.9126 (tmm) REVERT: C 736 MET cc_start: 0.9300 (mpp) cc_final: 0.8744 (mpp) REVERT: C 738 TYR cc_start: 0.9420 (t80) cc_final: 0.9086 (t80) REVERT: C 759 ASP cc_start: 0.9423 (t70) cc_final: 0.9147 (OUTLIER) REVERT: C 1085 MET cc_start: 0.9341 (ttp) cc_final: 0.9120 (tmm) outliers start: 7 outliers final: 4 residues processed: 45 average time/residue: 1.0283 time to fit residues: 49.8922 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 : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 710 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 45 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3178 r_free = 0.3178 target = 0.043822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.036346 restraints weight = 31912.415| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.99 r_work: 0.2792 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2521 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= 0.140 Angle : 0.469 9.479 8630 Z= 0.225 Chirality : 0.036 0.135 932 Planarity : 0.004 0.035 1114 Dihedral : 4.317 43.516 846 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.05 % Allowed : 7.68 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.31), residues: 746 helix: 3.04 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.55 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 932 HIS 0.002 0.000 HIS C1007 PHE 0.008 0.001 PHE B 739 TYR 0.007 0.001 TYR B1016 ARG 0.002 0.000 ARG C 862 *********************** 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 46 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 736 MET cc_start: 0.9346 (mpp) cc_final: 0.8814 (mpp) REVERT: B 738 TYR cc_start: 0.9414 (t80) cc_final: 0.9074 (t80) REVERT: B 759 ASP cc_start: 0.9389 (t70) cc_final: 0.9115 (OUTLIER) REVERT: B 903 GLU cc_start: 0.9307 (mm-30) cc_final: 0.9045 (mm-30) REVERT: B 1085 MET cc_start: 0.9345 (ttp) cc_final: 0.9120 (tmm) REVERT: C 736 MET cc_start: 0.9347 (mpp) cc_final: 0.8815 (mpp) REVERT: C 738 TYR cc_start: 0.9416 (t80) cc_final: 0.9077 (t80) REVERT: C 759 ASP cc_start: 0.9394 (t70) cc_final: 0.9110 (OUTLIER) REVERT: C 1085 MET cc_start: 0.9340 (ttp) cc_final: 0.9117 (tmm) outliers start: 7 outliers final: 6 residues processed: 43 average time/residue: 1.0129 time to fit residues: 46.8450 Evaluate side-chains 41 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 990 MET Chi-restraints excluded: chain D residue 560 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 0.1980 chunk 30 optimal weight: 4.9990 chunk 68 optimal weight: 0.0670 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.3199 r_free = 0.3199 target = 0.044448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.037027 restraints weight = 32099.260| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 4.01 r_work: 0.2813 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2661 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= 0.127 Angle : 0.491 10.340 8630 Z= 0.232 Chirality : 0.036 0.134 932 Planarity : 0.004 0.035 1114 Dihedral : 4.287 43.997 846 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.31), residues: 746 helix: 3.01 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.59 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 874 HIS 0.001 0.000 HIS B1007 PHE 0.008 0.001 PHE C 735 TYR 0.007 0.001 TYR C1016 ARG 0.002 0.000 ARG B 862 *********************** 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 49 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: B 736 MET cc_start: 0.9340 (tpp) cc_final: 0.8782 (mpp) REVERT: B 738 TYR cc_start: 0.9409 (t80) cc_final: 0.9021 (t80) REVERT: B 759 ASP cc_start: 0.9396 (t70) cc_final: 0.9131 (OUTLIER) REVERT: B 903 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9049 (mm-30) REVERT: B 990 MET cc_start: 0.9235 (mtm) cc_final: 0.8312 (mmm) REVERT: B 1085 MET cc_start: 0.9341 (ttp) cc_final: 0.9117 (tmm) REVERT: C 736 MET cc_start: 0.9338 (tpp) cc_final: 0.8775 (mpp) REVERT: C 738 TYR cc_start: 0.9408 (t80) cc_final: 0.9022 (t80) REVERT: C 759 ASP cc_start: 0.9392 (t70) cc_final: 0.9122 (OUTLIER) REVERT: C 903 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8891 (tp30) REVERT: C 944 MET cc_start: 0.8945 (mtm) cc_final: 0.8665 (mtm) REVERT: C 1085 MET cc_start: 0.9331 (ttp) cc_final: 0.9104 (tmm) outliers start: 6 outliers final: 5 residues processed: 47 average time/residue: 1.0114 time to fit residues: 51.1449 Evaluate side-chains 40 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE 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 47 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.044355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.036893 restraints weight = 31629.898| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.98 r_work: 0.2799 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2753 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= 0.147 Angle : 0.534 13.101 8630 Z= 0.246 Chirality : 0.037 0.160 932 Planarity : 0.004 0.035 1114 Dihedral : 4.289 44.591 846 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.05 % Allowed : 9.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.31), residues: 746 helix: 3.05 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.60 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 932 HIS 0.002 0.001 HIS B 836 PHE 0.008 0.001 PHE C 735 TYR 0.008 0.001 TYR B 830 ARG 0.002 0.000 ARG B 862 *********************** 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 47 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: B 736 MET cc_start: 0.9348 (tpp) cc_final: 0.8780 (mpp) REVERT: B 738 TYR cc_start: 0.9403 (t80) cc_final: 0.9039 (t80) REVERT: B 759 ASP cc_start: 0.9389 (t70) cc_final: 0.9148 (OUTLIER) REVERT: B 903 GLU cc_start: 0.9305 (mm-30) cc_final: 0.9016 (mm-30) REVERT: B 990 MET cc_start: 0.9266 (mtm) cc_final: 0.8337 (mmm) REVERT: B 1085 MET cc_start: 0.9336 (ttp) cc_final: 0.9102 (tmm) REVERT: C 736 MET cc_start: 0.9346 (tpp) cc_final: 0.8777 (mpp) REVERT: C 738 TYR cc_start: 0.9410 (t80) cc_final: 0.9049 (t80) REVERT: C 759 ASP cc_start: 0.9388 (t70) cc_final: 0.9145 (OUTLIER) REVERT: C 903 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8847 (tp30) REVERT: C 1085 MET cc_start: 0.9329 (ttp) cc_final: 0.9094 (tmm) outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 1.0115 time to fit residues: 47.8271 Evaluate side-chains 43 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE 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 16 optimal weight: 0.0370 chunk 31 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 29 optimal weight: 7.9990 chunk 60 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 75 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 740 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.045119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.037730 restraints weight = 32166.397| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.98 r_work: 0.2823 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 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 0.038 6358 Z= 0.135 Angle : 0.547 11.987 8630 Z= 0.250 Chirality : 0.037 0.146 932 Planarity : 0.004 0.035 1114 Dihedral : 4.272 44.690 846 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 0.75 % Allowed : 9.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.31), residues: 746 helix: 3.00 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.58 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 932 HIS 0.002 0.000 HIS B 836 PHE 0.013 0.001 PHE C 920 TYR 0.008 0.001 TYR C1016 ARG 0.002 0.000 ARG B 862 *********************** 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: 5 poor density : 40 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: B 736 MET cc_start: 0.9348 (tpp) cc_final: 0.8754 (mpp) REVERT: B 738 TYR cc_start: 0.9393 (t80) cc_final: 0.8987 (t80) REVERT: B 759 ASP cc_start: 0.9388 (t70) cc_final: 0.9138 (OUTLIER) REVERT: B 903 GLU cc_start: 0.9308 (mm-30) cc_final: 0.9025 (mm-30) REVERT: B 1085 MET cc_start: 0.9320 (ttp) cc_final: 0.9090 (tmm) REVERT: C 736 MET cc_start: 0.9338 (tpp) cc_final: 0.8737 (mpp) REVERT: C 738 TYR cc_start: 0.9414 (t80) cc_final: 0.9015 (t80) REVERT: C 759 ASP cc_start: 0.9382 (t70) cc_final: 0.9132 (OUTLIER) REVERT: C 903 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8835 (tp30) REVERT: C 1085 MET cc_start: 0.9313 (ttp) cc_final: 0.9082 (tmm) outliers start: 5 outliers final: 5 residues processed: 44 average time/residue: 1.0050 time to fit residues: 47.5737 Evaluate side-chains 42 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE 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 17 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3189 r_free = 0.3189 target = 0.044320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.036767 restraints weight = 32031.972| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 4.05 r_work: 0.2787 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6358 Z= 0.172 Angle : 0.562 12.445 8630 Z= 0.260 Chirality : 0.037 0.132 932 Planarity : 0.004 0.035 1114 Dihedral : 4.313 45.407 846 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.45 % Allowed : 9.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.31), residues: 746 helix: 3.03 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.55 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 932 HIS 0.002 0.001 HIS C 868 PHE 0.022 0.001 PHE C 920 TYR 0.011 0.001 TYR B 830 ARG 0.002 0.000 ARG B 862 ********************** 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: 3 poor density : 40 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: B 736 MET cc_start: 0.9359 (tpp) cc_final: 0.8789 (mpp) REVERT: B 738 TYR cc_start: 0.9423 (t80) cc_final: 0.9045 (t80) REVERT: B 759 ASP cc_start: 0.9381 (t70) cc_final: 0.9132 (OUTLIER) REVERT: B 903 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9035 (mm-30) REVERT: B 990 MET cc_start: 0.9313 (mmm) cc_final: 0.8898 (mmm) REVERT: C 736 MET cc_start: 0.9354 (tpp) cc_final: 0.8780 (mpp) REVERT: C 738 TYR cc_start: 0.9432 (t80) cc_final: 0.9062 (t80) REVERT: C 759 ASP cc_start: 0.9394 (t70) cc_final: 0.9143 (OUTLIER) REVERT: C 903 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8861 (tp30) outliers start: 3 outliers final: 5 residues processed: 42 average time/residue: 1.0563 time to fit residues: 47.5889 Evaluate side-chains 41 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE 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 4 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 0.5456 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.045040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.037672 restraints weight = 32144.346| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.01 r_work: 0.2822 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6358 Z= 0.145 Angle : 0.582 14.184 8630 Z= 0.261 Chirality : 0.037 0.134 932 Planarity : 0.004 0.035 1114 Dihedral : 4.259 45.150 846 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.75 % Allowed : 9.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.31), residues: 746 helix: 3.02 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.52 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 874 HIS 0.002 0.000 HIS C 836 PHE 0.027 0.001 PHE C 920 TYR 0.007 0.001 TYR C1016 ARG 0.002 0.000 ARG B 862 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3402.47 seconds wall clock time: 61 minutes 12.12 seconds (3672.12 seconds total)