Starting phenix.real_space_refine on Mon Mar 11 00:03:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/03_2024/7lrc_23494_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/03_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_23494/03_2024/7lrc_23494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/03_2024/7lrc_23494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/03_2024/7lrc_23494_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrc_23494/03_2024/7lrc_23494_updated.pdb" } 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 Residue "B PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6202 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2998 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 18, 'TRANS': 352} Chain breaks: 2 Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 79 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "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: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 79 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 1, ' MN': 1, 'X5M': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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} Time building chain proxies: 3.87, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 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... running ksdssp... Secondary structure from input PDB file: 42 helices and 2 sheets defined 63.3% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'B' and resid 680 through 682 No H-bonds generated for 'chain 'B' and resid 680 through 682' Processing helix chain 'B' and resid 685 through 690 removed outlier: 4.162A pdb=" N ASN B 690 " --> pdb=" O GLU B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 710 through 722 Processing helix chain 'B' and resid 724 through 727 No H-bonds generated for 'chain 'B' and resid 724 through 727' Processing helix chain 'B' and resid 732 through 745 Processing helix chain 'B' and resid 754 through 769 Processing helix chain 'B' and resid 817 through 819 No H-bonds generated for 'chain 'B' and resid 817 through 819' Processing helix chain 'B' and resid 823 through 834 Processing helix chain 'B' and resid 845 through 850 Processing helix chain 'B' and resid 854 through 858 Processing helix chain 'B' and resid 864 through 879 Processing helix chain 'B' and resid 881 through 883 No H-bonds generated for 'chain 'B' and resid 881 through 883' Processing helix chain 'B' and resid 891 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 913 through 925 Processing helix chain 'B' and resid 935 through 955 removed outlier: 3.585A pdb=" N ILE B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLY B 953 " --> pdb=" O ALA B 949 " (cutoff:3.500A) Proline residue: B 954 - end of helix Processing helix chain 'B' and resid 958 through 982 Processing helix chain 'B' and resid 997 through 1007 Processing helix chain 'B' and resid 1009 through 1019 Processing helix chain 'B' and resid 1074 through 1099 Processing helix chain 'A' and resid 552 through 558 Processing helix chain 'C' and resid 680 through 682 No H-bonds generated for 'chain 'C' and resid 680 through 682' Processing helix chain 'C' and resid 685 through 690 removed outlier: 4.163A pdb=" N ASN C 690 " --> pdb=" O GLU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 703 Processing helix chain 'C' and resid 710 through 722 Processing helix chain 'C' and resid 724 through 727 No H-bonds generated for 'chain 'C' and resid 724 through 727' Processing helix chain 'C' and resid 732 through 745 Processing helix chain 'C' and resid 754 through 769 Processing helix chain 'C' and resid 817 through 819 No H-bonds generated for 'chain 'C' and resid 817 through 819' Processing helix chain 'C' and resid 823 through 834 Processing helix chain 'C' and resid 845 through 850 Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 864 through 879 Processing helix chain 'C' and resid 881 through 883 No H-bonds generated for 'chain 'C' and resid 881 through 883' Processing helix chain 'C' and resid 891 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 913 through 925 Processing helix chain 'C' and resid 935 through 955 removed outlier: 3.585A pdb=" N ILE C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLY C 953 " --> pdb=" O ALA C 949 " (cutoff:3.500A) Proline residue: C 954 - end of helix Processing helix chain 'C' and resid 958 through 982 Processing helix chain 'C' and resid 997 through 1007 Processing helix chain 'C' and resid 1009 through 1019 Processing helix chain 'C' and resid 1074 through 1099 Processing helix chain 'D' and resid 552 through 558 Processing sheet with id= A, 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= B, first strand: chain 'C' and resid 1025 through 1027 removed outlier: 3.505A pdb=" N LYS C1070 " --> pdb=" O VAL C1027 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 930 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: 1.56 Time building geometry restraints manager: 2.42 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: 100.66 - 107.33: 260 107.33 - 114.00: 3524 114.00 - 120.67: 2797 120.67 - 127.34: 1957 127.34 - 134.00: 92 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: 30 2.42 - 3.04: 4066 3.04 - 3.66: 9321 3.66 - 4.28: 14640 4.28 - 4.90: 24181 Nonbonded interactions: 52238 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 52233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.820 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: 7.250 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.090 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.650 ------------------------------------------------------------------------------- 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= 0.162 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 : 0.692 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: 1.2431 time to fit residues: 94.3255 Evaluate side-chains 42 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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: 0.3980 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.0770 chunk 38 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 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: 0.7516 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6358 Z= 0.141 Angle : 0.454 7.102 8630 Z= 0.216 Chirality : 0.036 0.136 932 Planarity : 0.004 0.039 1114 Dihedral : 4.380 39.938 846 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.90 % Allowed : 7.83 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.31), residues: 746 helix: 2.80 (0.23), residues: 506 sheet: None (None), residues: 0 loop : 1.48 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 874 HIS 0.002 0.000 HIS C 868 PHE 0.008 0.001 PHE B 897 TYR 0.009 0.001 TYR A 555 ARG 0.004 0.000 ARG B 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 45 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.730 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 45 average time/residue: 0.9022 time to fit residues: 43.9181 Evaluate side-chains 40 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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: 0.9990 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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: 0.7597 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6358 Z= 0.201 Angle : 0.469 7.514 8630 Z= 0.227 Chirality : 0.036 0.136 932 Planarity : 0.003 0.040 1114 Dihedral : 4.444 43.013 846 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.81 % Allowed : 7.83 % 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: 3.73 (0.31), residues: 746 helix: 3.00 (0.23), residues: 494 sheet: None (None), residues: 0 loop : 1.51 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 874 HIS 0.003 0.001 HIS C 868 PHE 0.009 0.001 PHE B 739 TYR 0.007 0.001 TYR B 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 52 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.685 Fit side-chains REVERT: B 1085 MET cc_start: 0.7356 (tmm) cc_final: 0.6658 (ttp) REVERT: C 1085 MET cc_start: 0.7397 (tmm) cc_final: 0.6709 (ttp) outliers start: 12 outliers final: 8 residues processed: 52 average time/residue: 0.8120 time to fit residues: 45.9274 Evaluate side-chains 43 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 759 ASP Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 715 SER Chi-restraints excluded: chain C residue 759 ASP Chi-restraints excluded: chain C residue 861 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1866 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= 0.127 Angle : 0.455 7.876 8630 Z= 0.214 Chirality : 0.035 0.132 932 Planarity : 0.003 0.040 1114 Dihedral : 4.332 42.946 846 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.81 % Allowed : 7.68 % Favored : 90.51 % 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: 3.72 (0.31), residues: 746 helix: 2.94 (0.23), residues: 496 sheet: None (None), residues: 0 loop : 1.63 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 932 HIS 0.001 0.000 HIS B 868 PHE 0.008 0.001 PHE C 897 TYR 0.004 0.001 TYR B 766 ARG 0.002 0.000 ARG C 862 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 738 TYR cc_start: 0.6837 (t80) cc_final: 0.6517 (t80) REVERT: C 738 TYR cc_start: 0.6827 (t80) cc_final: 0.6510 (t80) outliers start: 12 outliers final: 6 residues processed: 47 average time/residue: 0.8644 time to fit residues: 43.9888 Evaluate side-chains 42 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 861 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: 0.6980 chunk 41 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 50 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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: 0.7546 moved from start: 0.2036 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= 0.119 Angle : 0.472 9.844 8630 Z= 0.216 Chirality : 0.035 0.133 932 Planarity : 0.003 0.040 1114 Dihedral : 4.223 44.100 846 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.26 % Allowed : 7.53 % 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: 2.99 (0.23), residues: 496 sheet: None (None), residues: 0 loop : 1.66 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 932 HIS 0.001 0.000 HIS C1007 PHE 0.008 0.001 PHE B 897 TYR 0.005 0.001 TYR C1016 ARG 0.002 0.000 ARG B 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 54 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 39 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 738 TYR cc_start: 0.7011 (t80) cc_final: 0.6672 (t80) REVERT: B 1085 MET cc_start: 0.7281 (tmm) cc_final: 0.6583 (ttp) REVERT: C 738 TYR cc_start: 0.7001 (t80) cc_final: 0.6666 (t80) REVERT: C 1085 MET cc_start: 0.7321 (tmm) cc_final: 0.6627 (ttp) outliers start: 15 outliers final: 6 residues processed: 49 average time/residue: 1.0265 time to fit residues: 54.0232 Evaluate side-chains 41 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 861 ASP 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: 5.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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: 0.7658 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6358 Z= 0.296 Angle : 0.576 13.443 8630 Z= 0.272 Chirality : 0.038 0.145 932 Planarity : 0.003 0.040 1114 Dihedral : 4.443 45.344 846 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.96 % Allowed : 8.13 % 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: 3.63 (0.30), residues: 746 helix: 2.88 (0.22), residues: 498 sheet: None (None), residues: 0 loop : 1.55 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 932 HIS 0.004 0.001 HIS C 868 PHE 0.022 0.001 PHE C 920 TYR 0.008 0.001 TYR B1016 ARG 0.002 0.000 ARG C 938 *********************** 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 47 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 34 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 738 TYR cc_start: 0.7107 (t80) cc_final: 0.6705 (t80) REVERT: B 1085 MET cc_start: 0.7298 (tmm) cc_final: 0.6677 (ttp) REVERT: C 738 TYR cc_start: 0.7095 (t80) cc_final: 0.6694 (t80) REVERT: C 1085 MET cc_start: 0.7337 (tmm) cc_final: 0.6721 (ttp) outliers start: 13 outliers final: 8 residues processed: 45 average time/residue: 0.9043 time to fit residues: 44.0301 Evaluate side-chains 42 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 715 SER Chi-restraints excluded: chain C residue 861 ASP 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: 7.9990 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7602 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6358 Z= 0.171 Angle : 0.543 10.699 8630 Z= 0.247 Chirality : 0.036 0.134 932 Planarity : 0.003 0.039 1114 Dihedral : 4.334 43.984 846 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.20 % Allowed : 8.73 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.31), residues: 746 helix: 2.96 (0.23), residues: 494 sheet: None (None), residues: 0 loop : 1.36 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 932 HIS 0.002 0.000 HIS B 868 PHE 0.017 0.001 PHE C 920 TYR 0.006 0.001 TYR B1016 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 45 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 738 TYR cc_start: 0.7035 (t80) cc_final: 0.6646 (t80) REVERT: C 738 TYR cc_start: 0.7024 (t80) cc_final: 0.6628 (t80) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.9626 time to fit residues: 44.6618 Evaluate side-chains 41 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 861 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 0.0870 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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: 0.7595 moved from start: 0.2534 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= 0.161 Angle : 0.577 12.544 8630 Z= 0.253 Chirality : 0.036 0.132 932 Planarity : 0.003 0.038 1114 Dihedral : 4.229 43.811 846 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.26 % Allowed : 7.98 % 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: 3.68 (0.31), residues: 746 helix: 3.01 (0.22), residues: 494 sheet: None (None), residues: 0 loop : 1.38 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 932 HIS 0.002 0.000 HIS B 868 PHE 0.016 0.001 PHE C 920 TYR 0.006 0.001 TYR B1016 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 51 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 738 TYR cc_start: 0.7046 (t80) cc_final: 0.6654 (t80) REVERT: B 1085 MET cc_start: 0.7173 (tmm) cc_final: 0.6680 (ttp) REVERT: C 738 TYR cc_start: 0.7040 (t80) cc_final: 0.6661 (t80) REVERT: C 1085 MET cc_start: 0.7212 (tmm) cc_final: 0.6726 (ttp) outliers start: 15 outliers final: 8 residues processed: 46 average time/residue: 0.9245 time to fit residues: 45.9162 Evaluate side-chains 43 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 715 SER Chi-restraints excluded: chain C residue 861 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.0170 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- 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: 0.7587 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6358 Z= 0.157 Angle : 0.578 12.659 8630 Z= 0.253 Chirality : 0.037 0.199 932 Planarity : 0.003 0.038 1114 Dihedral : 4.209 44.033 846 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.20 % Allowed : 9.34 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.61 (0.30), residues: 746 helix: 2.96 (0.22), residues: 494 sheet: None (None), residues: 0 loop : 1.35 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 932 HIS 0.002 0.001 HIS C 836 PHE 0.013 0.001 PHE C 920 TYR 0.006 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 43 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 738 TYR cc_start: 0.6992 (t80) cc_final: 0.6593 (t80) REVERT: B 1085 MET cc_start: 0.7149 (tmm) cc_final: 0.6557 (ttp) REVERT: C 738 TYR cc_start: 0.6984 (t80) cc_final: 0.6586 (t80) REVERT: C 1085 MET cc_start: 0.7179 (tmm) cc_final: 0.6591 (ttp) outliers start: 8 outliers final: 8 residues processed: 41 average time/residue: 0.9808 time to fit residues: 43.2735 Evaluate side-chains 41 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 715 SER Chi-restraints excluded: chain C residue 861 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 64 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 8 optimal weight: 0.0050 chunk 16 optimal weight: 3.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 740 HIS C 740 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2739 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= 0.141 Angle : 0.577 12.387 8630 Z= 0.252 Chirality : 0.036 0.163 932 Planarity : 0.003 0.039 1114 Dihedral : 4.163 44.145 846 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.51 % Allowed : 8.73 % 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: 3.64 (0.30), residues: 746 helix: 2.97 (0.22), residues: 494 sheet: None (None), residues: 0 loop : 1.37 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 874 HIS 0.002 0.000 HIS C 836 PHE 0.029 0.001 PHE C 920 TYR 0.005 0.001 TYR B1016 ARG 0.003 0.000 ARG C 898 ********************** 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 46 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 738 TYR cc_start: 0.6991 (t80) cc_final: 0.6597 (t80) REVERT: B 1085 MET cc_start: 0.7134 (tmm) cc_final: 0.6544 (ttp) REVERT: C 738 TYR cc_start: 0.6982 (t80) cc_final: 0.6582 (t80) REVERT: C 1085 MET cc_start: 0.7167 (tmm) cc_final: 0.6579 (ttp) outliers start: 10 outliers final: 8 residues processed: 44 average time/residue: 0.9457 time to fit residues: 44.9073 Evaluate side-chains 41 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 715 SER Chi-restraints excluded: chain C residue 861 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 53 optimal weight: 0.1980 chunk 3 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 51 optimal weight: 0.1980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.044093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.036517 restraints weight = 31860.045| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 4.03 r_work: 0.2801 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6358 Z= 0.152 Angle : 0.571 12.627 8630 Z= 0.250 Chirality : 0.036 0.157 932 Planarity : 0.003 0.038 1114 Dihedral : 4.167 44.536 846 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.51 % Allowed : 9.04 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.99 (0.22), residues: 494 sheet: None (None), residues: 0 loop : 1.35 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 874 HIS 0.002 0.000 HIS B 836 PHE 0.009 0.001 PHE C 920 TYR 0.005 0.001 TYR B1016 ARG 0.003 0.000 ARG B 898 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1913.50 seconds wall clock time: 35 minutes 8.34 seconds (2108.34 seconds total)