Starting phenix.real_space_refine on Tue Sep 24 10:21:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsp_27657/09_2024/8dsp_27657.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsp_27657/09_2024/8dsp_27657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsp_27657/09_2024/8dsp_27657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsp_27657/09_2024/8dsp_27657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsp_27657/09_2024/8dsp_27657.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsp_27657/09_2024/8dsp_27657.cif" } resolution = 3.3 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= 0.000 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 6 5.16 5 C 2425 2.51 5 N 709 2.21 5 O 757 1.98 5 H 3848 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7745 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2554 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 3, 'TRANS': 158} Chain: "E" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2596 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 3, 'TRANS': 160} Chain: "F" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2595 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 3, 'TRANS': 160} Time building chain proxies: 5.34, per 1000 atoms: 0.69 Number of scatterers: 7745 At special positions: 0 Unit cell: (80.1, 80.1, 87.576, 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 6 16.00 O 757 8.00 N 709 7.00 C 2425 6.00 H 3848 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 712.5 milliseconds 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 926 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 11 sheets defined 30.6% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 95 through 120 removed outlier: 3.646A pdb=" N LEU C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 156 removed outlier: 3.735A pdb=" N LEU C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 165 removed outlier: 3.563A pdb=" N SER C 161 " --> pdb=" O MET C 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 65 through 68 Processing helix chain 'E' and resid 95 through 120 removed outlier: 3.645A pdb=" N THR E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 166 removed outlier: 3.719A pdb=" N LEU E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER E 161 " --> pdb=" O MET E 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 65 through 68 Processing helix chain 'F' and resid 95 through 118 removed outlier: 3.817A pdb=" N LEU F 99 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR F 118 " --> pdb=" O ARG F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 167 Processing sheet with id=AA1, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.610A pdb=" N THR C 35 " --> pdb=" O GLU C 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 19 through 21 Processing sheet with id=AA3, first strand: chain 'C' and resid 122 through 123 removed outlier: 4.024A pdb=" N GLY C 122 " --> pdb=" O ASP C 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.943A pdb=" N GLY F 122 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 8 through 9 Processing sheet with id=AA6, first strand: chain 'E' and resid 8 through 9 Processing sheet with id=AA7, first strand: chain 'E' and resid 19 through 21 removed outlier: 7.294A pdb=" N THR E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.750A pdb=" N GLY E 122 " --> pdb=" O ASP E 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 19 through 21 removed outlier: 3.936A pdb=" N THR F 54 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N SER F 59 " --> pdb=" O PHE F 52 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE F 52 " --> pdb=" O SER F 59 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 42 through 43 removed outlier: 6.705A pdb=" N ILE F 37 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 42 through 43 135 hydrogen bonds defined for protein. 366 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 2.48 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: 3365 1.03 - 1.23: 488 1.23 - 1.42: 1647 1.42 - 1.62: 2290 1.62 - 1.81: 12 Bond restraints: 7802 Sorted by residual: bond pdb=" N ASP F 115 " pdb=" H ASP F 115 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" N LEU E 85 " pdb=" H LEU E 85 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N PHE C 52 " pdb=" H PHE C 52 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N THR F 120 " pdb=" H THR F 120 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N ILE F 121 " pdb=" H ILE F 121 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 ... (remaining 7797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 13376 1.44 - 2.89: 545 2.89 - 4.33: 87 4.33 - 5.77: 8 5.77 - 7.22: 3 Bond angle restraints: 14019 Sorted by residual: angle pdb=" CA VAL E 137 " pdb=" C VAL E 137 " pdb=" O VAL E 137 " ideal model delta sigma weight residual 120.80 116.27 4.53 8.90e-01 1.26e+00 2.59e+01 angle pdb=" CA VAL E 137 " pdb=" C VAL E 137 " pdb=" N ASN E 138 " ideal model delta sigma weight residual 117.15 121.08 -3.93 7.80e-01 1.64e+00 2.54e+01 angle pdb=" N VAL E 137 " pdb=" CA VAL E 137 " pdb=" C VAL E 137 " ideal model delta sigma weight residual 111.62 115.46 -3.84 7.90e-01 1.60e+00 2.36e+01 angle pdb=" N ASP C 49 " pdb=" CA ASP C 49 " pdb=" C ASP C 49 " ideal model delta sigma weight residual 113.41 107.49 5.92 1.22e+00 6.72e-01 2.36e+01 angle pdb=" N THR F 118 " pdb=" CA THR F 118 " pdb=" C THR F 118 " ideal model delta sigma weight residual 113.18 107.59 5.59 1.21e+00 6.83e-01 2.13e+01 ... (remaining 14014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 3257 16.02 - 32.04: 283 32.04 - 48.07: 63 48.07 - 64.09: 26 64.09 - 80.11: 2 Dihedral angle restraints: 3631 sinusoidal: 1999 harmonic: 1632 Sorted by residual: dihedral pdb=" CA TYR F 50 " pdb=" C TYR F 50 " pdb=" N ARG F 51 " pdb=" CA ARG F 51 " ideal model delta harmonic sigma weight residual 180.00 162.41 17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA GLN C 163 " pdb=" CB GLN C 163 " pdb=" CG GLN C 163 " pdb=" CD GLN C 163 " ideal model delta sinusoidal sigma weight residual 60.00 117.29 -57.29 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N SER E 92 " pdb=" CA SER E 92 " pdb=" CB SER E 92 " pdb=" OG SER E 92 " ideal model delta sinusoidal sigma weight residual -180.00 -123.29 -56.71 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 3628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 475 0.044 - 0.087: 86 0.087 - 0.131: 63 0.131 - 0.174: 13 0.174 - 0.218: 1 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA ILE E 136 " pdb=" N ILE E 136 " pdb=" C ILE E 136 " pdb=" CB ILE E 136 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE E 5 " pdb=" N ILE E 5 " pdb=" C ILE E 5 " pdb=" CB ILE E 5 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA ILE C 58 " pdb=" N ILE C 58 " pdb=" C ILE C 58 " pdb=" CB ILE C 58 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 635 not shown) Planarity restraints: 1171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 141 " -0.225 2.00e-02 2.50e+03 2.21e-01 7.35e+02 pdb=" CG ASN E 141 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN E 141 " 0.214 2.00e-02 2.50e+03 pdb=" ND2 ASN E 141 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN E 141 " 0.310 2.00e-02 2.50e+03 pdb="HD22 ASN E 141 " -0.318 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 163 " -0.187 2.00e-02 2.50e+03 1.81e-01 4.93e+02 pdb=" CD GLN C 163 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN C 163 " 0.175 2.00e-02 2.50e+03 pdb=" NE2 GLN C 163 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN C 163 " 0.252 2.00e-02 2.50e+03 pdb="HE22 GLN C 163 " -0.260 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 166 " 0.069 2.00e-02 2.50e+03 6.66e-02 6.66e+01 pdb=" CG ASN C 166 " -0.004 2.00e-02 2.50e+03 pdb=" OD1 ASN C 166 " -0.067 2.00e-02 2.50e+03 pdb=" ND2 ASN C 166 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 166 " -0.091 2.00e-02 2.50e+03 pdb="HD22 ASN C 166 " 0.095 2.00e-02 2.50e+03 ... (remaining 1168 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 701 2.21 - 2.81: 16662 2.81 - 3.40: 21289 3.40 - 4.00: 28031 4.00 - 4.60: 42205 Nonbonded interactions: 108888 Sorted by model distance: nonbonded pdb=" H ASN F 124 " pdb=" O HIS F 128 " model vdw 1.610 2.450 nonbonded pdb=" H LEU E 13 " pdb=" O THR E 71 " model vdw 1.623 2.450 nonbonded pdb=" OD1 ASN C 124 " pdb=" H ASN C 125 " model vdw 1.627 2.450 nonbonded pdb=" O ALA F 131 " pdb=" HE ARG F 134 " model vdw 1.663 2.450 nonbonded pdb=" O ARG E 165 " pdb="HH11 ARG E 165 " model vdw 1.676 2.450 ... (remaining 108883 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 'C' and (resid 6 through 78 or (resid 79 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB or \ name HG21 or name HG22 or name HG23)) or resid 80 through 162 or (resid 163 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ OE1 or name NE2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HE21 or name HE22)) or resid 164 through 167)) selection = (chain 'E' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ \ 1 or name HZ2 or name HZ3)) or (resid 7 and (name N or name CA or name C or name \ O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG \ 21 or name HG22 or name HG23)) or resid 8 through 156 or (resid 157 and (name N \ or name CA or name C or name O or name CB or name CG or name SD or name CE or na \ me H or name HA )) or resid 158 through 162 or (resid 163 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name OE1 or name NE2 or \ name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE \ 22)) or resid 164 through 167)) selection = (chain 'F' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ \ 1 or name HZ2 or name HZ3)) or resid 7 through 78 or (resid 79 and (name N or na \ me CA or name C or name O or name CB or name OG1 or name CG2 or name H or name H \ A or name HB or name HG21 or name HG22 or name HG23)) or resid 80 through 156 or \ (resid 157 and (name N or name CA or name C or name O or name CB or name CG or \ name SD or name CE or name H or name HA )) or resid 158 through 167)) } 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: 3.980 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: 0.150 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.800 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 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 : 0.005 0.038 3954 Z= 0.366 Angle : 0.794 7.218 5376 Z= 0.556 Chirality : 0.051 0.218 638 Planarity : 0.003 0.047 700 Dihedral : 12.778 80.110 1444 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.88 % Favored : 90.50 % Rotamer: Outliers : 0.47 % Allowed : 2.59 % Favored : 96.93 % 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: -1.65 (0.37), residues: 484 helix: 1.18 (0.45), residues: 126 sheet: -1.75 (0.69), residues: 61 loop : -2.09 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 162 HIS 0.001 0.000 HIS E 128 PHE 0.018 0.001 PHE E 24 TYR 0.018 0.001 TYR C 50 ARG 0.004 0.000 ARG C 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 THR cc_start: 0.7345 (m) cc_final: 0.6732 (m) REVERT: E 30 LYS cc_start: 0.8304 (ptmt) cc_final: 0.8056 (ptpp) REVERT: E 138 ASN cc_start: 0.6115 (p0) cc_final: 0.5701 (p0) REVERT: F 160 ASN cc_start: 0.7816 (t0) cc_final: 0.7513 (t0) outliers start: 2 outliers final: 1 residues processed: 139 average time/residue: 0.4115 time to fit residues: 69.6444 Evaluate side-chains 84 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 37 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 GLN ** C 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 HIS F 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3954 Z= 0.322 Angle : 0.739 7.024 5376 Z= 0.397 Chirality : 0.048 0.201 638 Planarity : 0.006 0.065 700 Dihedral : 5.053 28.918 548 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.50 % Favored : 89.88 % Rotamer: Outliers : 1.65 % Allowed : 14.86 % Favored : 83.49 % 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: -2.09 (0.35), residues: 484 helix: 0.47 (0.42), residues: 135 sheet: -2.05 (0.66), residues: 49 loop : -2.29 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 64 HIS 0.006 0.002 HIS E 128 PHE 0.025 0.002 PHE E 24 TYR 0.015 0.002 TYR E 26 ARG 0.007 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6405 (tm-30) REVERT: F 22 ILE cc_start: 0.7082 (mm) cc_final: 0.6871 (mt) outliers start: 7 outliers final: 6 residues processed: 86 average time/residue: 0.3847 time to fit residues: 39.9956 Evaluate side-chains 70 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 99 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 43 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN E 141 ASN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.7888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3954 Z= 0.307 Angle : 0.612 7.152 5376 Z= 0.342 Chirality : 0.044 0.159 638 Planarity : 0.004 0.038 700 Dihedral : 4.552 20.502 547 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.68 % Favored : 90.50 % Rotamer: Outliers : 0.94 % Allowed : 16.27 % Favored : 82.78 % 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: -1.78 (0.36), residues: 484 helix: 0.56 (0.41), residues: 132 sheet: -2.19 (0.59), residues: 57 loop : -1.88 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 162 HIS 0.004 0.001 HIS F 108 PHE 0.009 0.002 PHE C 151 TYR 0.012 0.002 TYR F 11 ARG 0.006 0.001 ARG E 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 35 THR cc_start: 0.7927 (t) cc_final: 0.7679 (t) REVERT: E 73 ILE cc_start: 0.8008 (mp) cc_final: 0.7777 (mt) REVERT: E 74 GLU cc_start: 0.7514 (tm-30) cc_final: 0.6858 (tm-30) REVERT: E 163 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8328 (tm-30) outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 0.3183 time to fit residues: 25.8742 Evaluate side-chains 57 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain F residue 9 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 GLN C 163 GLN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.9575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3954 Z= 0.308 Angle : 0.609 7.185 5376 Z= 0.334 Chirality : 0.044 0.144 638 Planarity : 0.005 0.052 700 Dihedral : 4.713 21.003 547 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.09 % Favored : 90.29 % Rotamer: Outliers : 1.42 % Allowed : 18.16 % Favored : 80.42 % 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: -1.72 (0.36), residues: 484 helix: 0.86 (0.43), residues: 129 sheet: -2.28 (0.63), residues: 49 loop : -1.95 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 64 HIS 0.005 0.001 HIS C 108 PHE 0.010 0.002 PHE C 52 TYR 0.008 0.001 TYR C 11 ARG 0.004 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7305 (tm-30) REVERT: E 163 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8334 (tm-30) outliers start: 6 outliers final: 4 residues processed: 58 average time/residue: 0.3220 time to fit residues: 24.0407 Evaluate side-chains 50 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 9 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.4980 chunk 19 optimal weight: 0.3980 chunk 39 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 0.0570 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 GLN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.9869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3954 Z= 0.207 Angle : 0.523 6.008 5376 Z= 0.288 Chirality : 0.041 0.126 638 Planarity : 0.004 0.035 700 Dihedral : 4.390 19.975 547 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.47 % Favored : 90.91 % Rotamer: Outliers : 1.18 % Allowed : 17.69 % Favored : 81.13 % 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: -1.44 (0.36), residues: 484 helix: 1.42 (0.44), residues: 123 sheet: -2.17 (0.65), residues: 49 loop : -1.86 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 64 HIS 0.001 0.000 HIS C 108 PHE 0.007 0.001 PHE F 24 TYR 0.007 0.001 TYR C 50 ARG 0.002 0.000 ARG E 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7235 (tm-30) REVERT: E 163 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8353 (tm-30) outliers start: 5 outliers final: 5 residues processed: 53 average time/residue: 0.3384 time to fit residues: 22.6839 Evaluate side-chains 53 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 9 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 GLN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 1.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3954 Z= 0.284 Angle : 0.547 5.378 5376 Z= 0.304 Chirality : 0.042 0.136 638 Planarity : 0.004 0.037 700 Dihedral : 4.520 19.506 547 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.62 % Allowed : 10.54 % Favored : 88.84 % Rotamer: Outliers : 2.36 % Allowed : 18.63 % Favored : 79.01 % 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: -1.61 (0.37), residues: 484 helix: 1.42 (0.44), residues: 123 sheet: -2.33 (0.55), residues: 71 loop : -1.94 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 64 HIS 0.002 0.001 HIS C 128 PHE 0.011 0.001 PHE C 52 TYR 0.010 0.001 TYR C 70 ARG 0.002 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 163 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8381 (tm-30) REVERT: F 74 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8503 (tm-30) outliers start: 10 outliers final: 7 residues processed: 49 average time/residue: 0.4234 time to fit residues: 27.0693 Evaluate side-chains 48 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 34 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 0.0020 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 1.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3954 Z= 0.193 Angle : 0.532 5.418 5376 Z= 0.291 Chirality : 0.041 0.131 638 Planarity : 0.003 0.032 700 Dihedral : 4.385 18.912 547 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.47 % Favored : 91.12 % Rotamer: Outliers : 1.42 % Allowed : 20.05 % Favored : 78.54 % 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: -1.28 (0.37), residues: 484 helix: 1.60 (0.45), residues: 123 sheet: -2.20 (0.58), residues: 64 loop : -1.69 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 162 HIS 0.001 0.000 HIS C 108 PHE 0.006 0.001 PHE C 24 TYR 0.010 0.001 TYR C 70 ARG 0.003 0.000 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 163 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8331 (tm-30) outliers start: 6 outliers final: 6 residues processed: 51 average time/residue: 0.3189 time to fit residues: 20.9114 Evaluate side-chains 49 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 34 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 chunk 18 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 GLN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 1.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3954 Z= 0.269 Angle : 0.559 6.920 5376 Z= 0.307 Chirality : 0.042 0.137 638 Planarity : 0.004 0.031 700 Dihedral : 4.449 19.134 547 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.74 % Favored : 88.84 % Rotamer: Outliers : 1.42 % Allowed : 20.28 % Favored : 78.30 % 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: -1.29 (0.37), residues: 484 helix: 1.51 (0.45), residues: 123 sheet: -1.76 (0.68), residues: 49 loop : -1.81 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 162 HIS 0.001 0.000 HIS C 128 PHE 0.009 0.001 PHE C 52 TYR 0.011 0.001 TYR C 70 ARG 0.002 0.000 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 163 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8397 (tm-30) outliers start: 6 outliers final: 6 residues processed: 48 average time/residue: 0.2653 time to fit residues: 17.0115 Evaluate side-chains 46 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.0670 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 42 optimal weight: 0.0970 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.0970 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 overall best weight: 0.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 GLN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 1.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3954 Z= 0.172 Angle : 0.517 5.662 5376 Z= 0.282 Chirality : 0.041 0.125 638 Planarity : 0.004 0.042 700 Dihedral : 4.272 18.228 547 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.68 % Favored : 90.91 % Rotamer: Outliers : 1.65 % Allowed : 20.05 % Favored : 78.30 % 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: -1.08 (0.37), residues: 484 helix: 1.67 (0.45), residues: 123 sheet: -1.85 (0.69), residues: 51 loop : -1.61 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 162 HIS 0.001 0.000 HIS C 108 PHE 0.005 0.001 PHE E 151 TYR 0.008 0.001 TYR C 70 ARG 0.002 0.000 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 163 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8376 (tm-30) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.3390 time to fit residues: 20.5295 Evaluate side-chains 48 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain F residue 9 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 30 optimal weight: 0.0770 chunk 40 optimal weight: 0.0770 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 GLN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 1.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3954 Z= 0.223 Angle : 0.531 5.645 5376 Z= 0.291 Chirality : 0.041 0.130 638 Planarity : 0.004 0.036 700 Dihedral : 4.282 17.753 547 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.50 % Favored : 90.08 % Rotamer: Outliers : 1.65 % Allowed : 19.34 % Favored : 79.01 % 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: -1.10 (0.38), residues: 484 helix: 1.87 (0.44), residues: 117 sheet: -1.57 (0.66), residues: 68 loop : -1.69 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 162 HIS 0.001 0.000 HIS F 108 PHE 0.007 0.001 PHE C 52 TYR 0.011 0.001 TYR C 70 ARG 0.002 0.000 ARG F 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue THR 79 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 163 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8377 (tm-30) outliers start: 7 outliers final: 7 residues processed: 48 average time/residue: 0.2478 time to fit residues: 16.2706 Evaluate side-chains 48 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 2 optimal weight: 0.0060 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 GLN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.078629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.069989 restraints weight = 39002.741| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.68 r_work: 0.3197 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 1.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3954 Z= 0.293 Angle : 0.554 5.051 5376 Z= 0.307 Chirality : 0.042 0.131 638 Planarity : 0.004 0.034 700 Dihedral : 4.501 19.219 547 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.33 % Favored : 89.26 % Rotamer: Outliers : 1.65 % Allowed : 19.58 % Favored : 78.77 % 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: -1.37 (0.37), residues: 484 helix: 1.40 (0.44), residues: 123 sheet: -1.99 (0.64), residues: 61 loop : -1.77 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 162 HIS 0.002 0.001 HIS F 108 PHE 0.010 0.001 PHE C 52 TYR 0.013 0.001 TYR C 70 ARG 0.002 0.000 ARG F 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3093.72 seconds wall clock time: 54 minutes 20.79 seconds (3260.79 seconds total)