Starting phenix.real_space_refine on Sun Dec 29 09:01:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bia_44585/12_2024/9bia_44585.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bia_44585/12_2024/9bia_44585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bia_44585/12_2024/9bia_44585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bia_44585/12_2024/9bia_44585.map" model { file = "/net/cci-nas-00/data/ceres_data/9bia_44585/12_2024/9bia_44585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bia_44585/12_2024/9bia_44585.cif" } resolution = 3.0 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= 0.012 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: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 3371 2.51 5 N 841 2.21 5 O 941 1.98 5 H 5263 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10430 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1735 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "C" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1688 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "A" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1735 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "D" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1718 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1777 Classifications: {'peptide': 118} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "F" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1777 Classifications: {'peptide': 118} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Time building chain proxies: 5.87, per 1000 atoms: 0.56 Number of scatterers: 10430 At special positions: 0 Unit cell: (67.252, 67.983, 108.188, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 941 8.00 N 841 7.00 C 3371 6.00 H 5263 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 99 " distance=2.03 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: 3.01 Conformation dependent library (CDL) restraints added in 756.3 milliseconds 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1248 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 5 sheets defined 60.1% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'B' and resid 37 through 71 removed outlier: 3.756A pdb=" N GLN B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 76 through 104 Processing helix chain 'B' and resid 111 through 141 Processing helix chain 'C' and resid 37 through 71 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 76 through 104 Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 111 through 139 Processing helix chain 'A' and resid 37 through 69 Processing helix chain 'A' and resid 70 through 74 removed outlier: 4.372A pdb=" N ASP A 73 " --> pdb=" O GLN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 102 Processing helix chain 'A' and resid 111 through 141 Processing helix chain 'D' and resid 37 through 71 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 76 through 104 Processing helix chain 'D' and resid 111 through 141 removed outlier: 3.524A pdb=" N PHE D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'F' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.432A pdb=" N GLY E 10 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG E 41 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU E 50 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.432A pdb=" N GLY E 10 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'F' and resid 61 through 63 removed outlier: 5.042A pdb=" N GLY F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA F 43 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARG F 53 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL F 37 " --> pdb=" O ARG F 53 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1164 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: 4.24 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5263 1.03 - 1.22: 0 1.22 - 1.42: 2210 1.42 - 1.61: 3031 1.61 - 1.80: 24 Bond restraints: 10528 Sorted by residual: bond pdb=" CB GLN A 91 " pdb=" CG GLN A 91 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.64e-01 bond pdb=" CB MET B 58 " pdb=" CG MET B 58 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 6.85e-01 bond pdb=" C LYS B 114 " pdb=" N LEU B 115 " ideal model delta sigma weight residual 1.335 1.325 0.010 1.31e-02 5.83e+03 6.23e-01 bond pdb=" CB PRO B 109 " pdb=" CG PRO B 109 " ideal model delta sigma weight residual 1.492 1.453 0.039 5.00e-02 4.00e+02 6.13e-01 bond pdb=" CA ARG C 34 " pdb=" C ARG C 34 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.10e-02 2.27e+03 6.11e-01 ... (remaining 10523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 17863 1.22 - 2.43: 1119 2.43 - 3.65: 37 3.65 - 4.87: 12 4.87 - 6.09: 1 Bond angle restraints: 19032 Sorted by residual: angle pdb=" N VAL F 116 " pdb=" CA VAL F 116 " pdb=" C VAL F 116 " ideal model delta sigma weight residual 109.34 115.43 -6.09 2.08e+00 2.31e-01 8.56e+00 angle pdb=" N GLN A 91 " pdb=" CA GLN A 91 " pdb=" CB GLN A 91 " ideal model delta sigma weight residual 110.20 106.83 3.37 1.49e+00 4.50e-01 5.11e+00 angle pdb=" N PRO A 109 " pdb=" CA PRO A 109 " pdb=" C PRO A 109 " ideal model delta sigma weight residual 112.47 116.83 -4.36 2.06e+00 2.36e-01 4.49e+00 angle pdb=" C VAL B 141 " pdb=" CA VAL B 141 " pdb=" CB VAL B 141 " ideal model delta sigma weight residual 111.29 108.03 3.26 1.64e+00 3.72e-01 3.95e+00 angle pdb=" CA GLN A 91 " pdb=" CB GLN A 91 " pdb=" CG GLN A 91 " ideal model delta sigma weight residual 114.10 117.86 -3.76 2.00e+00 2.50e-01 3.54e+00 ... (remaining 19027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4482 17.52 - 35.04: 296 35.04 - 52.55: 107 52.55 - 70.07: 53 70.07 - 87.59: 18 Dihedral angle restraints: 4956 sinusoidal: 2636 harmonic: 2320 Sorted by residual: dihedral pdb=" CA ASP E 76 " pdb=" C ASP E 76 " pdb=" N THR E 77 " pdb=" CA THR E 77 " ideal model delta harmonic sigma weight residual -180.00 -154.00 -26.00 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ILE C 36 " pdb=" C ILE C 36 " pdb=" N ASN C 37 " pdb=" CA ASN C 37 " ideal model delta harmonic sigma weight residual 180.00 155.79 24.21 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA GLN F 106 " pdb=" C GLN F 106 " pdb=" N TYR F 107 " pdb=" CA TYR F 107 " ideal model delta harmonic sigma weight residual 180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 4953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 542 0.031 - 0.062: 234 0.062 - 0.093: 47 0.093 - 0.124: 26 0.124 - 0.155: 6 Chirality restraints: 855 Sorted by residual: chirality pdb=" CA PRO A 109 " pdb=" N PRO A 109 " pdb=" C PRO A 109 " pdb=" CB PRO A 109 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA PRO B 109 " pdb=" N PRO B 109 " pdb=" C PRO B 109 " pdb=" CB PRO B 109 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA VAL E 40 " pdb=" N VAL E 40 " pdb=" C VAL E 40 " pdb=" CB VAL E 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 852 not shown) Planarity restraints: 1553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 113 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.35e+00 pdb=" C ALA B 113 " -0.053 2.00e-02 2.50e+03 pdb=" O ALA B 113 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS B 114 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 58 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C MET B 58 " 0.050 2.00e-02 2.50e+03 pdb=" O MET B 58 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA B 59 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 123 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C THR C 123 " -0.036 2.00e-02 2.50e+03 pdb=" O THR C 123 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY C 124 " 0.012 2.00e-02 2.50e+03 ... (remaining 1550 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 290 2.16 - 2.77: 20231 2.77 - 3.38: 30650 3.38 - 3.99: 38827 3.99 - 4.60: 61943 Nonbonded interactions: 151941 Sorted by model distance: nonbonded pdb=" HZ2 LYS B 44 " pdb=" OD1 ASN D 120 " model vdw 1.546 2.450 nonbonded pdb=" HZ2 LYS C 44 " pdb=" OD1 ASN A 120 " model vdw 1.568 2.450 nonbonded pdb=" OE1 GLU E 6 " pdb=" H GLU E 6 " model vdw 1.697 2.450 nonbonded pdb=" H ARG E 90 " pdb=" OD2 ASP E 93 " model vdw 1.707 2.450 nonbonded pdb=" OD1 ASP F 76 " pdb=" HG SER F 78 " model vdw 1.724 2.450 ... (remaining 151936 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' and resid 34 through 140) selection = (chain 'B' and resid 34 through 140) selection = chain 'C' selection = (chain 'D' and resid 34 through 140) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 1.850 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: 0.200 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.880 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 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 : 0.003 0.039 5265 Z= 0.228 Angle : 0.604 6.087 7161 Z= 0.380 Chirality : 0.039 0.155 855 Planarity : 0.005 0.031 905 Dihedral : 13.715 87.588 1837 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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: 0.99 (0.30), residues: 660 helix: 1.07 (0.23), residues: 355 sheet: 0.15 (0.50), residues: 116 loop : 0.48 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 39 HIS 0.011 0.002 HIS B 112 PHE 0.014 0.001 PHE D 74 TYR 0.021 0.004 TYR E 36 ARG 0.002 0.000 ARG F 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: C 57 LEU cc_start: 0.7684 (tt) cc_final: 0.7477 (tt) REVERT: A 51 MET cc_start: 0.7949 (mmp) cc_final: 0.7705 (mmm) REVERT: D 103 LYS cc_start: 0.8154 (tttt) cc_final: 0.7551 (ttmt) REVERT: D 114 LYS cc_start: 0.5866 (mmtp) cc_final: 0.5469 (mmpt) REVERT: E 20 LEU cc_start: 0.8503 (mt) cc_final: 0.8248 (mm) REVERT: E 28 ASN cc_start: 0.8345 (m-40) cc_final: 0.7673 (t0) REVERT: E 83 TYR cc_start: 0.7646 (m-80) cc_final: 0.7443 (m-80) REVERT: E 102 TYR cc_start: 0.6702 (t80) cc_final: 0.6066 (t80) REVERT: F 18 LEU cc_start: 0.6622 (mt) cc_final: 0.6421 (mt) REVERT: F 46 LYS cc_start: 0.7403 (mttt) cc_final: 0.6670 (tmmt) REVERT: F 88 SER cc_start: 0.7053 (m) cc_final: 0.6755 (t) REVERT: F 115 LEU cc_start: 0.8175 (mp) cc_final: 0.7881 (mm) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 1.9374 time to fit residues: 207.1882 Evaluate side-chains 77 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5265 Z= 0.323 Angle : 0.532 5.771 7161 Z= 0.295 Chirality : 0.040 0.157 855 Planarity : 0.004 0.039 905 Dihedral : 4.559 22.206 716 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.33 % Allowed : 6.81 % Favored : 90.86 % 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: 2.46 (0.31), residues: 660 helix: 2.51 (0.24), residues: 355 sheet: 0.55 (0.57), residues: 94 loop : 0.74 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 39 HIS 0.008 0.001 HIS B 112 PHE 0.009 0.001 PHE D 74 TYR 0.013 0.002 TYR E 107 ARG 0.004 0.001 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.907 Fit side-chains REVERT: B 51 MET cc_start: 0.7335 (mmp) cc_final: 0.7075 (mmp) REVERT: C 49 GLU cc_start: 0.7471 (tt0) cc_final: 0.7232 (mt-10) REVERT: A 51 MET cc_start: 0.7919 (mmp) cc_final: 0.7638 (mmm) REVERT: D 103 LYS cc_start: 0.8102 (tttt) cc_final: 0.7506 (ttmt) REVERT: D 105 ASP cc_start: 0.7735 (t0) cc_final: 0.7310 (t0) REVERT: D 114 LYS cc_start: 0.5949 (mmtp) cc_final: 0.5554 (mmpt) REVERT: E 28 ASN cc_start: 0.8366 (m-40) cc_final: 0.7707 (t0) REVERT: E 83 TYR cc_start: 0.7822 (m-80) cc_final: 0.7582 (m-80) REVERT: E 94 THR cc_start: 0.7774 (t) cc_final: 0.7445 (m) REVERT: F 46 LYS cc_start: 0.7303 (mttt) cc_final: 0.6621 (tmmt) REVERT: F 79 LYS cc_start: 0.7623 (ptmm) cc_final: 0.7364 (ptpp) REVERT: F 115 LEU cc_start: 0.8093 (mp) cc_final: 0.7775 (mm) outliers start: 13 outliers final: 4 residues processed: 83 average time/residue: 1.6891 time to fit residues: 150.2871 Evaluate side-chains 81 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 3 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5265 Z= 0.189 Angle : 0.458 4.913 7161 Z= 0.250 Chirality : 0.038 0.142 855 Planarity : 0.003 0.036 905 Dihedral : 4.077 20.749 716 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.61 % Allowed : 8.96 % Favored : 89.43 % 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: 3.03 (0.31), residues: 660 helix: 3.03 (0.24), residues: 357 sheet: 0.59 (0.57), residues: 94 loop : 0.94 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 39 HIS 0.005 0.001 HIS B 112 PHE 0.008 0.001 PHE E 71 TYR 0.011 0.001 TYR E 35 ARG 0.004 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 GLU cc_start: 0.7337 (tt0) cc_final: 0.7047 (mt-10) REVERT: A 51 MET cc_start: 0.7891 (mmp) cc_final: 0.7595 (mmm) REVERT: D 103 LYS cc_start: 0.8029 (tttt) cc_final: 0.7483 (ttmt) REVERT: D 105 ASP cc_start: 0.7729 (t0) cc_final: 0.7115 (t0) REVERT: D 114 LYS cc_start: 0.5916 (mmtp) cc_final: 0.5487 (mmpt) REVERT: E 28 ASN cc_start: 0.8375 (m-40) cc_final: 0.7667 (t0) REVERT: E 83 TYR cc_start: 0.7824 (m-80) cc_final: 0.7574 (m-80) REVERT: E 93 ASP cc_start: 0.7648 (m-30) cc_final: 0.7203 (m-30) REVERT: F 46 LYS cc_start: 0.7252 (mttt) cc_final: 0.6518 (tmmt) outliers start: 9 outliers final: 4 residues processed: 87 average time/residue: 1.8585 time to fit residues: 171.9400 Evaluate side-chains 83 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 3 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.0270 chunk 43 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5265 Z= 0.171 Angle : 0.440 4.349 7161 Z= 0.239 Chirality : 0.038 0.138 855 Planarity : 0.003 0.033 905 Dihedral : 3.817 19.816 716 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.33 % Allowed : 8.96 % Favored : 88.71 % 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: 3.31 (0.31), residues: 660 helix: 3.35 (0.23), residues: 357 sheet: 0.55 (0.56), residues: 94 loop : 0.98 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 39 HIS 0.003 0.001 HIS B 112 PHE 0.005 0.001 PHE D 127 TYR 0.013 0.001 TYR E 35 ARG 0.002 0.000 ARG F 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.7231 (mmp) cc_final: 0.6958 (mmp) REVERT: C 49 GLU cc_start: 0.7329 (tt0) cc_final: 0.7060 (mt-10) REVERT: A 51 MET cc_start: 0.7933 (mmp) cc_final: 0.7519 (mmm) REVERT: D 103 LYS cc_start: 0.8015 (tttt) cc_final: 0.7466 (ttmt) REVERT: D 105 ASP cc_start: 0.7700 (t0) cc_final: 0.7212 (t0) REVERT: E 28 ASN cc_start: 0.8369 (m-40) cc_final: 0.7657 (t0) REVERT: E 83 TYR cc_start: 0.7848 (m-80) cc_final: 0.7599 (m-80) REVERT: E 93 ASP cc_start: 0.7667 (m-30) cc_final: 0.7277 (m-30) REVERT: F 46 LYS cc_start: 0.7230 (mttt) cc_final: 0.6513 (tmmt) REVERT: F 68 LYS cc_start: 0.6976 (tppt) cc_final: 0.6692 (ttmt) outliers start: 13 outliers final: 5 residues processed: 82 average time/residue: 1.6872 time to fit residues: 147.4799 Evaluate side-chains 82 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain E residue 110 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 15 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN A 33 ASN D 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5265 Z= 0.221 Angle : 0.450 4.417 7161 Z= 0.244 Chirality : 0.038 0.136 855 Planarity : 0.003 0.034 905 Dihedral : 3.911 23.273 716 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.61 % Allowed : 10.22 % Favored : 88.17 % 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: 3.33 (0.31), residues: 660 helix: 3.39 (0.23), residues: 358 sheet: 0.53 (0.55), residues: 94 loop : 0.95 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 39 HIS 0.003 0.001 HIS B 112 PHE 0.006 0.001 PHE F 71 TYR 0.013 0.001 TYR E 35 ARG 0.003 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.7309 (mmp) cc_final: 0.6996 (mmp) REVERT: C 49 GLU cc_start: 0.7409 (tt0) cc_final: 0.7120 (mt-10) REVERT: A 51 MET cc_start: 0.7905 (mmp) cc_final: 0.7486 (mmm) REVERT: D 103 LYS cc_start: 0.8024 (tttt) cc_final: 0.7470 (ttmt) REVERT: D 105 ASP cc_start: 0.7652 (t0) cc_final: 0.7233 (t0) REVERT: E 28 ASN cc_start: 0.8388 (m-40) cc_final: 0.7676 (t0) REVERT: E 83 TYR cc_start: 0.7862 (m-80) cc_final: 0.7581 (m-80) REVERT: E 93 ASP cc_start: 0.7695 (m-30) cc_final: 0.7326 (m-30) REVERT: F 46 LYS cc_start: 0.7201 (mttt) cc_final: 0.6495 (tmmt) REVERT: F 68 LYS cc_start: 0.7021 (tppt) cc_final: 0.6758 (ttmt) outliers start: 9 outliers final: 5 residues processed: 77 average time/residue: 1.7167 time to fit residues: 141.2157 Evaluate side-chains 79 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain E residue 110 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN D 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5265 Z= 0.185 Angle : 0.439 4.392 7161 Z= 0.238 Chirality : 0.038 0.135 855 Planarity : 0.003 0.035 905 Dihedral : 3.880 33.039 716 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.15 % Allowed : 10.04 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 3.46 (0.31), residues: 660 helix: 3.52 (0.22), residues: 358 sheet: 0.55 (0.55), residues: 94 loop : 0.98 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 39 HIS 0.003 0.001 HIS D 112 PHE 0.009 0.001 PHE F 71 TYR 0.015 0.001 TYR E 35 ARG 0.002 0.000 ARG F 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.7302 (mmp) cc_final: 0.6987 (mmp) REVERT: C 49 GLU cc_start: 0.7372 (tt0) cc_final: 0.7097 (mt-10) REVERT: A 51 MET cc_start: 0.7879 (mmp) cc_final: 0.7470 (mmm) REVERT: D 103 LYS cc_start: 0.8022 (tttt) cc_final: 0.7449 (ttmt) REVERT: D 105 ASP cc_start: 0.7679 (t0) cc_final: 0.7210 (t0) REVERT: E 66 SER cc_start: 0.8899 (t) cc_final: 0.8174 (p) REVERT: E 83 TYR cc_start: 0.7866 (m-80) cc_final: 0.7633 (m-80) REVERT: E 93 ASP cc_start: 0.7713 (m-30) cc_final: 0.7366 (m-30) REVERT: F 46 LYS cc_start: 0.7187 (mttt) cc_final: 0.6500 (tmmt) REVERT: F 68 LYS cc_start: 0.7058 (tppt) cc_final: 0.6800 (ttmt) outliers start: 12 outliers final: 6 residues processed: 78 average time/residue: 1.6653 time to fit residues: 138.7089 Evaluate side-chains 75 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 3 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 ASN D 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5265 Z= 0.176 Angle : 0.433 4.432 7161 Z= 0.234 Chirality : 0.037 0.135 855 Planarity : 0.003 0.034 905 Dihedral : 3.613 18.895 716 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.79 % Allowed : 10.22 % Favored : 87.99 % 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: 3.50 (0.31), residues: 660 helix: 3.63 (0.22), residues: 358 sheet: 0.36 (0.54), residues: 98 loop : 0.95 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 39 HIS 0.006 0.001 HIS D 112 PHE 0.009 0.001 PHE F 71 TYR 0.018 0.001 TYR E 35 ARG 0.003 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.7315 (mmp) cc_final: 0.7047 (mmp) REVERT: C 49 GLU cc_start: 0.7374 (tt0) cc_final: 0.7100 (mt-10) REVERT: A 51 MET cc_start: 0.7872 (mmp) cc_final: 0.7481 (mmm) REVERT: D 103 LYS cc_start: 0.8020 (tttt) cc_final: 0.7452 (ttmt) REVERT: D 105 ASP cc_start: 0.7694 (t0) cc_final: 0.7274 (t0) REVERT: E 66 SER cc_start: 0.8907 (t) cc_final: 0.8179 (p) REVERT: E 83 TYR cc_start: 0.7883 (m-80) cc_final: 0.7624 (m-80) REVERT: E 93 ASP cc_start: 0.7704 (m-30) cc_final: 0.7373 (m-30) REVERT: F 19 ARG cc_start: 0.8349 (ttm170) cc_final: 0.8148 (ttt90) REVERT: F 46 LYS cc_start: 0.7181 (mttt) cc_final: 0.6490 (tmmt) REVERT: F 68 LYS cc_start: 0.7083 (tppt) cc_final: 0.6792 (ttmt) outliers start: 10 outliers final: 6 residues processed: 80 average time/residue: 1.7903 time to fit residues: 152.4128 Evaluate side-chains 75 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 3 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.0010 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 ASN D 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5265 Z= 0.251 Angle : 0.454 4.476 7161 Z= 0.246 Chirality : 0.038 0.135 855 Planarity : 0.003 0.036 905 Dihedral : 3.622 19.482 716 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.61 % Allowed : 11.29 % Favored : 87.10 % 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: 3.30 (0.31), residues: 660 helix: 3.46 (0.22), residues: 359 sheet: 0.32 (0.53), residues: 98 loop : 0.84 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 39 HIS 0.002 0.001 HIS A 112 PHE 0.008 0.001 PHE C 135 TYR 0.019 0.001 TYR E 35 ARG 0.002 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.7389 (mmp) cc_final: 0.7147 (mmp) REVERT: A 51 MET cc_start: 0.7878 (mmp) cc_final: 0.7513 (mmm) REVERT: D 103 LYS cc_start: 0.8039 (tttt) cc_final: 0.7465 (ttmt) REVERT: D 105 ASP cc_start: 0.7831 (t0) cc_final: 0.7515 (t0) REVERT: E 66 SER cc_start: 0.8922 (t) cc_final: 0.8188 (p) REVERT: E 83 TYR cc_start: 0.7878 (m-80) cc_final: 0.7651 (m-80) REVERT: F 19 ARG cc_start: 0.8317 (ttm170) cc_final: 0.8108 (ttt90) REVERT: F 46 LYS cc_start: 0.7166 (mttt) cc_final: 0.6521 (tmmt) outliers start: 9 outliers final: 5 residues processed: 78 average time/residue: 1.7713 time to fit residues: 147.6631 Evaluate side-chains 74 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 3 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN D 70 GLN E 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5265 Z= 0.189 Angle : 0.441 4.501 7161 Z= 0.239 Chirality : 0.038 0.135 855 Planarity : 0.003 0.034 905 Dihedral : 3.525 19.023 716 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.43 % Allowed : 12.90 % Favored : 85.66 % 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: 3.40 (0.31), residues: 660 helix: 3.55 (0.22), residues: 359 sheet: 0.41 (0.53), residues: 98 loop : 0.83 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 39 HIS 0.002 0.001 HIS B 112 PHE 0.009 0.001 PHE F 71 TYR 0.013 0.001 TYR E 35 ARG 0.002 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.7379 (mmp) cc_final: 0.7138 (mmp) REVERT: C 49 GLU cc_start: 0.7417 (tt0) cc_final: 0.7158 (mt-10) REVERT: A 51 MET cc_start: 0.7853 (mmp) cc_final: 0.7490 (mmm) REVERT: D 103 LYS cc_start: 0.8047 (tttt) cc_final: 0.7471 (ttmt) REVERT: D 105 ASP cc_start: 0.7824 (t0) cc_final: 0.7485 (t0) REVERT: E 66 SER cc_start: 0.8925 (t) cc_final: 0.8188 (p) REVERT: E 83 TYR cc_start: 0.7866 (m-80) cc_final: 0.7647 (m-80) REVERT: F 19 ARG cc_start: 0.8314 (ttm170) cc_final: 0.8102 (ttt90) REVERT: F 46 LYS cc_start: 0.7166 (mttt) cc_final: 0.6514 (tmmt) outliers start: 8 outliers final: 6 residues processed: 76 average time/residue: 1.7195 time to fit residues: 139.4074 Evaluate side-chains 75 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 3 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN D 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5265 Z= 0.209 Angle : 0.447 5.296 7161 Z= 0.241 Chirality : 0.038 0.135 855 Planarity : 0.003 0.035 905 Dihedral : 3.510 19.071 716 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.08 % Allowed : 13.26 % Favored : 85.66 % 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: 3.40 (0.31), residues: 660 helix: 3.56 (0.22), residues: 359 sheet: 0.46 (0.53), residues: 98 loop : 0.79 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 39 HIS 0.002 0.001 HIS B 112 PHE 0.021 0.001 PHE F 71 TYR 0.015 0.001 TYR E 35 ARG 0.002 0.000 ARG E 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.7384 (mmp) cc_final: 0.7134 (mmp) REVERT: C 49 GLU cc_start: 0.7427 (tt0) cc_final: 0.7185 (mt-10) REVERT: A 51 MET cc_start: 0.7872 (mmp) cc_final: 0.7507 (mmm) REVERT: D 103 LYS cc_start: 0.8045 (tttt) cc_final: 0.7468 (ttmt) REVERT: D 105 ASP cc_start: 0.7810 (t0) cc_final: 0.7473 (t0) REVERT: E 66 SER cc_start: 0.8929 (t) cc_final: 0.8171 (p) REVERT: E 83 TYR cc_start: 0.7867 (m-80) cc_final: 0.7614 (m-80) REVERT: F 19 ARG cc_start: 0.8259 (ttm170) cc_final: 0.8045 (ttt90) REVERT: F 46 LYS cc_start: 0.7144 (mttt) cc_final: 0.6487 (tmmt) REVERT: F 68 LYS cc_start: 0.7046 (tppt) cc_final: 0.6820 (ttmt) outliers start: 6 outliers final: 5 residues processed: 74 average time/residue: 1.8071 time to fit residues: 142.4994 Evaluate side-chains 75 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 3 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN D 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.138203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103518 restraints weight = 15932.801| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.83 r_work: 0.3069 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5265 Z= 0.191 Angle : 0.439 4.868 7161 Z= 0.237 Chirality : 0.038 0.134 855 Planarity : 0.003 0.034 905 Dihedral : 3.461 18.874 716 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 0.91 % Favored : 98.94 % Rotamer: Outliers : 1.61 % Allowed : 12.54 % Favored : 85.84 % 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: 3.44 (0.31), residues: 660 helix: 3.60 (0.22), residues: 359 sheet: 0.47 (0.52), residues: 98 loop : 0.80 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 39 HIS 0.002 0.001 HIS B 112 PHE 0.014 0.001 PHE F 71 TYR 0.015 0.001 TYR E 35 ARG 0.002 0.000 ARG F 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4164.62 seconds wall clock time: 75 minutes 0.47 seconds (4500.47 seconds total)