Starting phenix.real_space_refine on Tue Sep 24 00:22:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/09_2024/7lrc_23494.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/09_2024/7lrc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/09_2024/7lrc_23494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/09_2024/7lrc_23494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/09_2024/7lrc_23494.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/09_2024/7lrc_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-5461/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: 5.61, per 1000 atoms: 0.90 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: 1.69 Conformation dependent library (CDL) restraints added in 935.6 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: 0.64 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: 1.62 Time building geometry restraints manager: 1.94 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.660 Find NCS groups from input model: 0.170 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.880 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.719 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: 1.2136 time to fit residues: 92.0863 Evaluate side-chains 42 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 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 fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.595 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 53 average time/residue: 0.6874 time to fit residues: 39.4732 Evaluate side-chains 40 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 710 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 0.2980 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 0.0970 chunk 55 optimal weight: 0.5980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1074 GLN C1074 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6358 Z= 0.117 Angle : 0.455 7.626 8630 Z= 0.222 Chirality : 0.036 0.134 932 Planarity : 0.004 0.034 1114 Dihedral : 4.442 39.479 846 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.65 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: 3.66 (0.30), residues: 746 helix: 2.89 (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 0.009 0.001 TRP B1026 HIS 0.001 0.000 HIS C1007 PHE 0.010 0.001 PHE C 897 TYR 0.010 0.001 TYR C 738 ARG 0.003 0.000 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 54 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.702 Fit side-chains outliers start: 11 outliers final: 2 residues processed: 50 average time/residue: 0.9561 time to fit residues: 51.3238 Evaluate side-chains 37 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 710 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6358 Z= 0.235 Angle : 0.516 7.745 8630 Z= 0.254 Chirality : 0.038 0.132 932 Planarity : 0.004 0.035 1114 Dihedral : 4.493 42.539 846 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.20 % Allowed : 8.58 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.76 (0.31), residues: 746 helix: 3.02 (0.23), residues: 514 sheet: None (None), residues: 0 loop : 1.36 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 932 HIS 0.004 0.001 HIS C 868 PHE 0.007 0.001 PHE C 739 TYR 0.011 0.001 TYR B1016 ARG 0.003 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 45 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.720 Fit side-chains REVERT: B 738 TYR cc_start: 0.6864 (t80) cc_final: 0.6554 (t80) REVERT: B 878 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.6502 (mpt) REVERT: B 1085 MET cc_start: 0.7365 (tmm) cc_final: 0.6657 (ttp) REVERT: C 738 TYR cc_start: 0.6851 (t80) cc_final: 0.6532 (t80) REVERT: C 878 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6514 (mpt) REVERT: C 1085 MET cc_start: 0.7411 (tmm) cc_final: 0.6703 (ttp) outliers start: 8 outliers final: 4 residues processed: 42 average time/residue: 1.0059 time to fit residues: 45.5500 Evaluate side-chains 40 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 759 ASP Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 759 ASP 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 61 optimal weight: 0.0010 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.0170 chunk 54 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6358 Z= 0.127 Angle : 0.486 9.907 8630 Z= 0.232 Chirality : 0.036 0.134 932 Planarity : 0.004 0.036 1114 Dihedral : 4.432 42.305 846 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.36 % Allowed : 7.53 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.66 (0.31), residues: 746 helix: 2.95 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.30 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C1026 HIS 0.002 0.000 HIS B 836 PHE 0.009 0.001 PHE B 897 TYR 0.007 0.001 TYR C 738 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 fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.721 Fit side-chains REVERT: B 738 TYR cc_start: 0.7022 (t80) cc_final: 0.6628 (t80) REVERT: B 878 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.6393 (mpt) REVERT: B 1085 MET cc_start: 0.7314 (tmm) cc_final: 0.6583 (ttp) REVERT: C 738 TYR cc_start: 0.7000 (t80) cc_final: 0.6603 (t80) REVERT: C 878 MET cc_start: 0.6622 (OUTLIER) cc_final: 0.6412 (mpt) REVERT: C 1085 MET cc_start: 0.7360 (tmm) cc_final: 0.6630 (ttp) outliers start: 9 outliers final: 2 residues processed: 44 average time/residue: 0.9396 time to fit residues: 44.6160 Evaluate side-chains 39 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 878 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 61 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6358 Z= 0.196 Angle : 0.505 9.466 8630 Z= 0.244 Chirality : 0.037 0.138 932 Planarity : 0.004 0.035 1114 Dihedral : 4.431 43.752 846 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.90 % Allowed : 8.43 % 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: 3.69 (0.31), residues: 746 helix: 2.97 (0.23), residues: 514 sheet: None (None), residues: 0 loop : 1.33 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 932 HIS 0.002 0.001 HIS C1007 PHE 0.008 0.001 PHE B 739 TYR 0.008 0.001 TYR B1016 ARG 0.002 0.000 ARG B 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 44 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.763 Fit side-chains REVERT: B 738 TYR cc_start: 0.6965 (t80) cc_final: 0.6593 (t80) REVERT: C 738 TYR cc_start: 0.6957 (t80) cc_final: 0.6583 (t80) outliers start: 6 outliers final: 2 residues processed: 42 average time/residue: 1.1372 time to fit residues: 51.3403 Evaluate side-chains 38 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 710 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 61 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6358 Z= 0.171 Angle : 0.546 10.306 8630 Z= 0.255 Chirality : 0.037 0.138 932 Planarity : 0.004 0.036 1114 Dihedral : 4.395 44.152 846 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.90 % Allowed : 9.49 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.69 (0.31), residues: 746 helix: 2.93 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.43 (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 B 868 PHE 0.011 0.001 PHE C 920 TYR 0.008 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 43 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.660 Fit side-chains REVERT: B 738 TYR cc_start: 0.7013 (t80) cc_final: 0.6616 (t80) REVERT: B 1085 MET cc_start: 0.7240 (tmm) cc_final: 0.6763 (ttp) REVERT: C 738 TYR cc_start: 0.7003 (t80) cc_final: 0.6607 (t80) REVERT: C 1085 MET cc_start: 0.7288 (tmm) cc_final: 0.6811 (ttp) outliers start: 6 outliers final: 2 residues processed: 41 average time/residue: 1.0175 time to fit residues: 44.8523 Evaluate side-chains 36 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 710 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6358 Z= 0.170 Angle : 0.573 12.367 8630 Z= 0.262 Chirality : 0.037 0.136 932 Planarity : 0.004 0.035 1114 Dihedral : 4.374 44.471 846 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 3.65 (0.31), residues: 746 helix: 2.90 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.41 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 874 HIS 0.002 0.000 HIS B1007 PHE 0.017 0.001 PHE C 920 TYR 0.008 0.001 TYR C1016 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 38 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.708 Fit side-chains REVERT: B 738 TYR cc_start: 0.6994 (t80) cc_final: 0.6587 (t80) REVERT: B 1085 MET cc_start: 0.7236 (tmm) cc_final: 0.6669 (ttp) REVERT: C 738 TYR cc_start: 0.6984 (t80) cc_final: 0.6575 (t80) REVERT: C 1085 MET cc_start: 0.7288 (tmm) cc_final: 0.6720 (ttp) outliers start: 4 outliers final: 4 residues processed: 38 average time/residue: 1.0739 time to fit residues: 43.7729 Evaluate side-chains 36 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 1090 ILE Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 1090 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.0980 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 0.0870 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6358 Z= 0.146 Angle : 0.578 11.826 8630 Z= 0.261 Chirality : 0.036 0.138 932 Planarity : 0.004 0.036 1114 Dihedral : 4.314 44.273 846 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.60 % Allowed : 9.64 % 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: 3.66 (0.31), residues: 746 helix: 2.91 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.41 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 932 HIS 0.001 0.000 HIS C 836 PHE 0.026 0.001 PHE C 920 TYR 0.008 0.001 TYR B1016 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 41 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.854 Fit side-chains REVERT: B 738 TYR cc_start: 0.7008 (t80) cc_final: 0.6599 (t80) REVERT: B 835 MET cc_start: 0.6359 (pmm) cc_final: 0.6145 (ptp) REVERT: B 1085 MET cc_start: 0.7170 (tmm) cc_final: 0.6397 (ttp) REVERT: C 738 TYR cc_start: 0.7062 (t80) cc_final: 0.6644 (t80) REVERT: C 1085 MET cc_start: 0.7257 (tmm) cc_final: 0.6505 (ttp) outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.9608 time to fit residues: 42.5028 Evaluate side-chains 36 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 710 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 4.9990 chunk 60 optimal weight: 0.2980 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3056 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= 0.156 Angle : 0.587 13.306 8630 Z= 0.266 Chirality : 0.037 0.139 932 Planarity : 0.004 0.035 1114 Dihedral : 4.319 44.573 846 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.39 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: 3.62 (0.31), residues: 746 helix: 2.88 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.40 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 932 HIS 0.002 0.000 HIS C 868 PHE 0.008 0.001 PHE C 739 TYR 0.007 0.001 TYR B1016 ARG 0.002 0.000 ARG C 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 42 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.769 Fit side-chains REVERT: B 738 TYR cc_start: 0.7093 (t80) cc_final: 0.6654 (t80) REVERT: B 1085 MET cc_start: 0.7227 (tmm) cc_final: 0.6475 (ttp) REVERT: C 738 TYR cc_start: 0.7008 (t80) cc_final: 0.6592 (t80) REVERT: C 1085 MET cc_start: 0.7267 (tmm) cc_final: 0.6518 (ttp) outliers start: 6 outliers final: 4 residues processed: 40 average time/residue: 0.9116 time to fit residues: 39.5182 Evaluate side-chains 39 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 1090 ILE Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 1090 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3224 r_free = 0.3224 target = 0.045561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.037998 restraints weight = 31544.043| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.08 r_work: 0.2836 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3125 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= 0.146 Angle : 0.575 13.410 8630 Z= 0.259 Chirality : 0.037 0.139 932 Planarity : 0.004 0.035 1114 Dihedral : 4.297 44.626 846 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 0.60 % Allowed : 9.49 % 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: 3.60 (0.31), residues: 746 helix: 2.88 (0.22), residues: 514 sheet: None (None), residues: 0 loop : 1.38 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 932 HIS 0.002 0.000 HIS C 756 PHE 0.013 0.001 PHE C 920 TYR 0.011 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: 1784.29 seconds wall clock time: 41 minutes 18.56 seconds (2478.56 seconds total)