Starting phenix.real_space_refine on Tue Mar 11 16:39:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lrc_23494/03_2025/7lrc_23494.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lrc_23494/03_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_23494/03_2025/7lrc_23494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lrc_23494/03_2025/7lrc_23494.map" model { file = "/net/cci-nas-00/data/ceres_data/7lrc_23494/03_2025/7lrc_23494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lrc_23494/03_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-5624/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: 5.55, per 1000 atoms: 0.89 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: 1.97 Conformation dependent library (CDL) restraints added in 965.6 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 73.8% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 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: 2.28 Time building geometry restraints manager: 2.12 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: 0.04 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: 1.640 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.690 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:15.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.820 ------------------------------------------------------------------------------- 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 : 0.758 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: 1.2672 time to fit residues: 96.0601 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 : 0.725 ------------------------------------------------------------------------------- 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 = 0.037522 restraints weight = 31790.337| |-----------------------------------------------------------------------------| 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 : 0.763 Fit side-chains REVERT: B 802 VAL cc_start: 0.9091 (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: 0.9291 (ttp) cc_final: 0.9078 (tmm) outliers start: 10 outliers final: 2 residues processed: 53 average time/residue: 0.8684 time to fit residues: 50.0089 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 : 0.768 ------------------------------------------------------------------------------- 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: 6.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 68 optimal weight: 0.0060 chunk 16 optimal weight: 0.6980 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 693 ASN B 999 ASN B1074 GLN C 693 ASN C 999 ASN C1074 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.043604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.035973 restraints weight = 32717.254| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.96 r_work: 0.2763 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1942 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= 0.181 Angle : 0.476 8.071 8630 Z= 0.235 Chirality : 0.037 0.135 932 Planarity : 0.004 0.035 1114 Dihedral : 4.522 41.084 846 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.66 % Allowed : 6.78 % 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 (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: 3.73 (0.30), residues: 746 helix: 2.96 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.46 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1026 HIS 0.003 0.001 HIS B 868 PHE 0.009 0.001 PHE B 739 TYR 0.010 0.001 TYR B1016 ARG 0.003 0.000 ARG B 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 53 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.763 Fit side-chains REVERT: B 736 MET cc_start: 0.9321 (mpp) cc_final: 0.8836 (mpp) REVERT: B 802 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8909 (p) REVERT: B 1085 MET cc_start: 0.9289 (ttp) cc_final: 0.9075 (tmm) REVERT: C 736 MET cc_start: 0.9330 (mpp) cc_final: 0.8854 (mpp) REVERT: C 944 MET cc_start: 0.9263 (tpp) cc_final: 0.9029 (mtp) REVERT: C 1085 MET cc_start: 0.9281 (ttp) cc_final: 0.9063 (tmm) outliers start: 11 outliers final: 2 residues processed: 51 average time/residue: 0.9877 time to fit residues: 54.1514 Evaluate side-chains 38 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.0040 chunk 20 optimal weight: 0.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.043703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.036061 restraints weight = 32994.740| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.02 r_work: 0.2768 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6358 Z= 0.163 Angle : 0.458 8.152 8630 Z= 0.228 Chirality : 0.037 0.138 932 Planarity : 0.004 0.036 1114 Dihedral : 4.415 42.199 846 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.20 % Allowed : 7.98 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.79 (0.31), residues: 746 helix: 3.02 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.45 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 932 HIS 0.003 0.001 HIS C 868 PHE 0.008 0.001 PHE C 739 TYR 0.008 0.001 TYR B1016 ARG 0.002 0.000 ARG B 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 44 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.954 Fit side-chains REVERT: B 736 MET cc_start: 0.9312 (mpp) cc_final: 0.8786 (mpp) REVERT: B 738 TYR cc_start: 0.9388 (t80) cc_final: 0.9071 (t80) REVERT: B 759 ASP cc_start: 0.9436 (t70) cc_final: 0.9174 (OUTLIER) REVERT: B 878 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8091 (mpt) REVERT: B 990 MET cc_start: 0.9216 (mtm) cc_final: 0.8240 (mmm) REVERT: C 736 MET cc_start: 0.9319 (mpp) cc_final: 0.8796 (mpp) REVERT: C 738 TYR cc_start: 0.9388 (t80) cc_final: 0.9071 (t80) REVERT: C 759 ASP cc_start: 0.9435 (t70) cc_final: 0.9174 (OUTLIER) REVERT: C 878 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8100 (mpt) REVERT: C 990 MET cc_start: 0.9213 (mtm) cc_final: 0.8243 (mmm) REVERT: C 1085 MET cc_start: 0.9279 (ttp) cc_final: 0.9078 (tmm) outliers start: 8 outliers final: 4 residues processed: 41 average time/residue: 1.1792 time to fit residues: 51.8082 Evaluate side-chains 40 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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: 0.4980 chunk 74 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 23 optimal weight: 0.0670 chunk 16 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.044283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.036685 restraints weight = 32587.893| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.98 r_work: 0.2796 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6358 Z= 0.123 Angle : 0.460 9.857 8630 Z= 0.222 Chirality : 0.036 0.133 932 Planarity : 0.004 0.035 1114 Dihedral : 4.339 43.266 846 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.90 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 (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: 3.84 (0.31), residues: 746 helix: 3.04 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.50 (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 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 52 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.916 Fit side-chains REVERT: B 736 MET cc_start: 0.9308 (mpp) cc_final: 0.8767 (mpp) REVERT: B 738 TYR cc_start: 0.9399 (t80) cc_final: 0.9055 (t80) REVERT: B 759 ASP cc_start: 0.9411 (t70) cc_final: 0.9148 (OUTLIER) REVERT: C 736 MET cc_start: 0.9290 (mpp) cc_final: 0.8749 (mpp) REVERT: C 738 TYR cc_start: 0.9404 (t80) cc_final: 0.9069 (t80) REVERT: C 759 ASP cc_start: 0.9417 (t70) cc_final: 0.9158 (OUTLIER) REVERT: C 1085 MET cc_start: 0.9267 (ttp) cc_final: 0.9050 (tmm) outliers start: 10 outliers final: 4 residues processed: 48 average time/residue: 1.0345 time to fit residues: 53.7308 Evaluate side-chains 40 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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: 3.9990 chunk 60 optimal weight: 0.3980 chunk 43 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 37 optimal weight: 0.1980 chunk 53 optimal weight: 0.3980 chunk 26 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.045074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.037455 restraints weight = 31997.402| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 4.04 r_work: 0.2819 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6358 Z= 0.114 Angle : 0.475 9.482 8630 Z= 0.227 Chirality : 0.036 0.139 932 Planarity : 0.004 0.034 1114 Dihedral : 4.300 43.800 846 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.20 % Allowed : 7.83 % 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 (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 : 1.57 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 932 HIS 0.002 0.000 HIS C1007 PHE 0.020 0.001 PHE C 920 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 49 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 736 MET cc_start: 0.9300 (mpp) cc_final: 0.8726 (mpp) REVERT: B 738 TYR cc_start: 0.9423 (t80) cc_final: 0.9090 (t80) REVERT: B 759 ASP cc_start: 0.9423 (t70) cc_final: 0.9151 (OUTLIER) REVERT: C 736 MET cc_start: 0.9304 (mpp) cc_final: 0.8732 (mpp) REVERT: C 738 TYR cc_start: 0.9432 (t80) cc_final: 0.9106 (t80) REVERT: C 759 ASP cc_start: 0.9446 (t70) cc_final: 0.9181 (OUTLIER) REVERT: C 903 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8931 (tp30) REVERT: C 1085 MET cc_start: 0.9279 (ttp) cc_final: 0.9059 (tmm) outliers start: 8 outliers final: 6 residues processed: 45 average time/residue: 1.1574 time to fit residues: 55.8365 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 : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 990 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 990 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 68 optimal weight: 0.0270 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 = 0.3202 r_free = 0.3202 target = 0.044712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.037012 restraints weight = 32457.383| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 4.05 r_work: 0.2805 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2693 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= 0.151 Angle : 0.508 10.319 8630 Z= 0.240 Chirality : 0.037 0.138 932 Planarity : 0.004 0.034 1114 Dihedral : 4.291 44.719 846 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 3.02 (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 0.008 0.001 TRP C 874 HIS 0.002 0.000 HIS B1007 PHE 0.022 0.001 PHE C 920 TYR 0.007 0.001 TYR B 830 ARG 0.002 0.000 ARG C 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 46 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 736 MET cc_start: 0.9320 (tpp) cc_final: 0.8767 (mpp) REVERT: B 738 TYR cc_start: 0.9418 (t80) cc_final: 0.9039 (t80) REVERT: B 759 ASP cc_start: 0.9422 (t70) cc_final: 0.9155 (OUTLIER) REVERT: C 736 MET cc_start: 0.9310 (tpp) cc_final: 0.8754 (mpp) REVERT: C 738 TYR cc_start: 0.9416 (t80) cc_final: 0.9039 (t80) REVERT: C 759 ASP cc_start: 0.9433 (t70) cc_final: 0.9169 (OUTLIER) REVERT: C 903 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8880 (tp30) outliers start: 6 outliers final: 6 residues processed: 44 average time/residue: 1.1603 time to fit residues: 54.7326 Evaluate side-chains 43 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 990 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 990 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3158 r_free = 0.3158 target = 0.043321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.035795 restraints weight = 31520.099| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.99 r_work: 0.2757 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6358 Z= 0.238 Angle : 0.589 12.978 8630 Z= 0.273 Chirality : 0.038 0.136 932 Planarity : 0.004 0.035 1114 Dihedral : 4.412 45.389 846 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.20 % Allowed : 8.58 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.78 (0.31), residues: 746 helix: 2.98 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.54 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 932 HIS 0.003 0.001 HIS B 868 PHE 0.022 0.001 PHE C 920 TYR 0.006 0.001 TYR C 859 ARG 0.002 0.000 ARG C 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 46 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 736 MET cc_start: 0.9393 (tpp) cc_final: 0.8871 (mpp) REVERT: B 738 TYR cc_start: 0.9448 (t80) cc_final: 0.9089 (t80) REVERT: B 759 ASP cc_start: 0.9413 (t70) cc_final: 0.9130 (OUTLIER) REVERT: C 736 MET cc_start: 0.9390 (tpp) cc_final: 0.8867 (mpp) REVERT: C 738 TYR cc_start: 0.9460 (t80) cc_final: 0.9100 (t80) REVERT: C 759 ASP cc_start: 0.9416 (t70) cc_final: 0.9140 (OUTLIER) REVERT: C 903 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8897 (tp30) REVERT: C 1085 MET cc_start: 0.9305 (ttp) cc_final: 0.9087 (tmm) outliers start: 8 outliers final: 7 residues processed: 42 average time/residue: 1.1126 time to fit residues: 49.9737 Evaluate side-chains 42 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 16 optimal weight: 0.0570 chunk 31 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 11 optimal weight: 0.0170 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 = 0.3216 r_free = 0.3216 target = 0.045392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.037830 restraints weight = 31491.412| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 4.05 r_work: 0.2824 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 6358 Z= 0.142 Angle : 0.562 12.003 8630 Z= 0.257 Chirality : 0.037 0.143 932 Planarity : 0.004 0.035 1114 Dihedral : 4.320 44.831 846 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.90 % Allowed : 9.19 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.99 (0.22), residues: 510 sheet: None (None), residues: 0 loop : 1.52 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1086 HIS 0.002 0.000 HIS B 836 PHE 0.018 0.001 PHE C 920 TYR 0.009 0.001 TYR C 830 ARG 0.002 0.000 ARG C 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 47 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 736 MET cc_start: 0.9347 (tpp) cc_final: 0.8770 (mpp) REVERT: B 738 TYR cc_start: 0.9417 (t80) cc_final: 0.9076 (t80) REVERT: B 759 ASP cc_start: 0.9373 (t70) cc_final: 0.9101 (OUTLIER) REVERT: B 1085 MET cc_start: 0.9302 (ttp) cc_final: 0.8938 (pp-130) REVERT: C 736 MET cc_start: 0.9348 (tpp) cc_final: 0.8772 (mpp) REVERT: C 738 TYR cc_start: 0.9404 (t80) cc_final: 0.9068 (t80) REVERT: C 759 ASP cc_start: 0.9382 (t70) cc_final: 0.9120 (OUTLIER) REVERT: C 903 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8833 (tp30) outliers start: 6 outliers final: 6 residues processed: 44 average time/residue: 0.9754 time to fit residues: 46.4418 Evaluate side-chains 44 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 990 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 990 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.0980 chunk 70 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 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 = 0.3188 r_free = 0.3188 target = 0.044524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036637 restraints weight = 32103.136| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.16 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6358 Z= 0.175 Angle : 0.593 14.020 8630 Z= 0.267 Chirality : 0.037 0.134 932 Planarity : 0.003 0.034 1114 Dihedral : 4.341 45.576 846 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.75 % Allowed : 9.04 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.80 (0.31), residues: 746 helix: 3.03 (0.22), residues: 510 sheet: None (None), residues: 0 loop : 1.48 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 874 HIS 0.002 0.001 HIS B 868 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 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 44 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 736 MET cc_start: 0.9182 (tpp) cc_final: 0.8601 (mpp) REVERT: B 738 TYR cc_start: 0.9371 (t80) cc_final: 0.8967 (t80) REVERT: B 759 ASP cc_start: 0.9085 (t70) cc_final: 0.8815 (OUTLIER) REVERT: B 1085 MET cc_start: 0.9098 (ttp) cc_final: 0.8769 (pp-130) REVERT: C 736 MET cc_start: 0.9186 (tpp) cc_final: 0.8596 (mpp) REVERT: C 738 TYR cc_start: 0.9379 (t80) cc_final: 0.9033 (t80) REVERT: C 759 ASP cc_start: 0.9068 (t70) cc_final: 0.8788 (OUTLIER) REVERT: C 903 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8391 (tp30) outliers start: 5 outliers final: 7 residues processed: 42 average time/residue: 0.9623 time to fit residues: 43.8110 Evaluate side-chains 44 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.0570 chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 0.0270 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 0.0670 chunk 54 optimal weight: 0.5980 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 740 HIS B 999 ASN C 740 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.045613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.038145 restraints weight = 31874.254| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 4.01 r_work: 0.2839 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3042 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= 0.126 Angle : 0.572 13.630 8630 Z= 0.254 Chirality : 0.036 0.139 932 Planarity : 0.004 0.035 1114 Dihedral : 4.238 44.974 846 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.60 % Allowed : 9.19 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.05 (0.22), residues: 510 sheet: None (None), residues: 0 loop : 1.47 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 874 HIS 0.002 0.000 HIS B 756 PHE 0.008 0.001 PHE C 735 TYR 0.012 0.001 TYR C 830 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: 3570.58 seconds wall clock time: 61 minutes 58.33 seconds (3718.33 seconds total)