Starting phenix.real_space_refine on Tue Feb 13 20:52:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsp_27657/02_2024/8dsp_27657.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsp_27657/02_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_27657/02_2024/8dsp_27657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsp_27657/02_2024/8dsp_27657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsp_27657/02_2024/8dsp_27657.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsp_27657/02_2024/8dsp_27657.pdb" } 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 Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "E TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 111": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 3.87, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.57 Conformation dependent library (CDL) restraints added in 815.6 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: 0.71 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: 2.69 Time building geometry restraints manager: 6.80 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: 100.43 - 107.15: 112 107.15 - 113.88: 9223 113.88 - 120.60: 2637 120.60 - 127.32: 2022 127.32 - 134.04: 25 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 1.850 nonbonded pdb=" H LEU E 13 " pdb=" O THR E 71 " model vdw 1.623 1.850 nonbonded pdb=" OD1 ASN C 124 " pdb=" H ASN C 125 " model vdw 1.627 1.850 nonbonded pdb=" O ALA F 131 " pdb=" HE ARG F 134 " model vdw 1.663 1.850 nonbonded pdb=" O ARG E 165 " pdb="HH11 ARG E 165 " model vdw 1.676 1.850 ... (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 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: 3.340 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: 0.110 Extract box with map and model: 12.940 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 29.310 Find NCS groups from input model: 0.390 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: 49.000 ------------------------------------------------------------------------------- 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 : 0.638 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: 0.3795 time to fit residues: 63.3446 Evaluate side-chains 84 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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: 0.8980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 HIS F 103 GLN ** 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: 0.7574 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3954 Z= 0.336 Angle : 0.733 9.251 5376 Z= 0.390 Chirality : 0.048 0.179 638 Planarity : 0.006 0.073 700 Dihedral : 4.978 20.669 548 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.71 % Favored : 89.46 % Rotamer: Outliers : 2.83 % Allowed : 12.26 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.36), residues: 484 helix: 0.88 (0.44), residues: 132 sheet: -2.12 (0.66), residues: 49 loop : -2.30 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 64 HIS 0.005 0.001 HIS E 108 PHE 0.025 0.003 PHE F 52 TYR 0.015 0.002 TYR E 26 ARG 0.006 0.001 ARG C 55 *********************** 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 96 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.645 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: E 74 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6395 (tm-30) outliers start: 12 outliers final: 8 residues processed: 91 average time/residue: 0.4015 time to fit residues: 44.3010 Evaluate side-chains 77 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 19 ASP Chi-restraints excluded: chain F residue 27 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: 0.9990 chunk 13 optimal weight: 0.0470 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 12 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 0.0670 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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: 0.7730 moved from start: 0.6787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3954 Z= 0.219 Angle : 0.538 6.901 5376 Z= 0.296 Chirality : 0.041 0.152 638 Planarity : 0.003 0.039 700 Dihedral : 4.354 18.611 547 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.47 % Favored : 90.70 % Rotamer: Outliers : 1.89 % Allowed : 14.86 % Favored : 83.25 % 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: -1.75 (0.36), residues: 484 helix: 1.14 (0.44), residues: 135 sheet: -1.98 (0.60), residues: 57 loop : -2.25 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 162 HIS 0.001 0.000 HIS F 108 PHE 0.008 0.001 PHE E 24 TYR 0.009 0.001 TYR C 70 ARG 0.003 0.000 ARG C 135 *********************** 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 77 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 ILE cc_start: 0.7942 (mp) cc_final: 0.7658 (mt) REVERT: E 74 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6672 (tm-30) REVERT: E 163 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8272 (tm-30) REVERT: F 11 TYR cc_start: 0.7726 (m-80) cc_final: 0.7317 (m-80) outliers start: 8 outliers final: 5 residues processed: 73 average time/residue: 0.3382 time to fit residues: 30.9401 Evaluate side-chains 69 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 54 THR 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: 0.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.9403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 3954 Z= 0.396 Angle : 0.653 6.997 5376 Z= 0.363 Chirality : 0.045 0.144 638 Planarity : 0.005 0.040 700 Dihedral : 4.871 20.474 547 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.30 % Favored : 89.88 % Rotamer: Outliers : 2.83 % Allowed : 16.51 % Favored : 80.66 % 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: -2.00 (0.36), residues: 484 helix: 1.02 (0.46), residues: 129 sheet: -1.90 (0.60), residues: 64 loop : -2.44 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 64 HIS 0.003 0.001 HIS F 108 PHE 0.012 0.002 PHE C 52 TYR 0.020 0.002 TYR C 70 ARG 0.006 0.001 ARG F 76 *********************** 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 66 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7194 (tm-30) REVERT: E 163 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8438 (tm-30) REVERT: F 11 TYR cc_start: 0.8772 (m-80) cc_final: 0.8476 (m-80) REVERT: F 104 ILE cc_start: 0.9157 (tp) cc_final: 0.8933 (tp) outliers start: 12 outliers final: 7 residues processed: 64 average time/residue: 0.3014 time to fit residues: 24.7999 Evaluate side-chains 54 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 99 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 41 optimal weight: 0.0870 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.9767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3954 Z= 0.199 Angle : 0.523 4.685 5376 Z= 0.288 Chirality : 0.041 0.129 638 Planarity : 0.003 0.035 700 Dihedral : 4.415 21.244 547 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.85 % Favored : 91.53 % Rotamer: Outliers : 2.12 % Allowed : 16.75 % 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: -1.64 (0.36), residues: 484 helix: 1.16 (0.44), residues: 129 sheet: -1.85 (0.65), residues: 57 loop : -2.08 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 64 HIS 0.002 0.001 HIS C 108 PHE 0.007 0.001 PHE C 151 TYR 0.008 0.001 TYR F 97 ARG 0.003 0.000 ARG E 41 *********************** 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 62 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 ILE cc_start: 0.9180 (mm) cc_final: 0.8937 (mt) REVERT: E 74 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7233 (tm-30) REVERT: E 163 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8427 (tm-30) REVERT: F 11 TYR cc_start: 0.8705 (m-80) cc_final: 0.8293 (m-80) REVERT: F 74 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8070 (tm-30) REVERT: F 104 ILE cc_start: 0.9095 (tp) cc_final: 0.8852 (tp) outliers start: 9 outliers final: 7 residues processed: 58 average time/residue: 0.3223 time to fit residues: 23.9499 Evaluate side-chains 56 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 37 ILE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 99 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 1.0582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3954 Z= 0.349 Angle : 0.574 4.750 5376 Z= 0.322 Chirality : 0.042 0.137 638 Planarity : 0.004 0.033 700 Dihedral : 4.609 20.248 547 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.92 % Favored : 89.26 % Rotamer: Outliers : 1.89 % Allowed : 19.10 % 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: -1.76 (0.36), residues: 484 helix: 1.11 (0.45), residues: 129 sheet: -1.85 (0.66), residues: 57 loop : -2.20 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 64 HIS 0.002 0.001 HIS E 108 PHE 0.011 0.001 PHE C 52 TYR 0.009 0.001 TYR F 97 ARG 0.004 0.000 ARG F 76 *********************** 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 53 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8529 (mpp) REVERT: F 11 TYR cc_start: 0.8859 (m-80) cc_final: 0.8554 (m-80) REVERT: F 74 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8137 (tm-30) REVERT: F 104 ILE cc_start: 0.9160 (tp) cc_final: 0.8902 (tp) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 0.2812 time to fit residues: 18.4178 Evaluate side-chains 49 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 117 THR 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: 0.9980 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 1.0762 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= 0.206 Angle : 0.545 7.147 5376 Z= 0.297 Chirality : 0.041 0.124 638 Planarity : 0.003 0.028 700 Dihedral : 4.447 20.531 547 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.06 % Favored : 91.32 % Rotamer: Outliers : 1.18 % Allowed : 19.58 % Favored : 79.25 % 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: -1.33 (0.37), residues: 484 helix: 1.54 (0.45), residues: 123 sheet: -1.59 (0.68), residues: 57 loop : -1.89 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 64 HIS 0.001 0.000 HIS F 108 PHE 0.007 0.001 PHE C 20 TYR 0.008 0.001 TYR F 97 ARG 0.003 0.000 ARG F 76 *********************** 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 51 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8641 (mpp) REVERT: F 11 TYR cc_start: 0.8790 (m-80) cc_final: 0.8453 (m-80) REVERT: F 74 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8063 (tm-30) REVERT: F 104 ILE cc_start: 0.9105 (tp) cc_final: 0.8848 (tp) outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.2812 time to fit residues: 17.3726 Evaluate side-chains 50 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 107 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 1.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3954 Z= 0.288 Angle : 0.584 9.841 5376 Z= 0.320 Chirality : 0.041 0.133 638 Planarity : 0.004 0.030 700 Dihedral : 4.510 20.365 547 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.62 % Allowed : 10.74 % Favored : 88.64 % Rotamer: Outliers : 1.18 % Allowed : 20.28 % 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: -1.34 (0.37), residues: 484 helix: 1.51 (0.45), residues: 123 sheet: -1.37 (0.73), residues: 54 loop : -1.94 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 64 HIS 0.001 0.000 HIS C 128 PHE 0.009 0.001 PHE C 52 TYR 0.010 0.001 TYR C 11 ARG 0.003 0.000 ARG F 76 *********************** 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 51 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 11 TYR cc_start: 0.8855 (m-80) cc_final: 0.8490 (m-80) REVERT: F 104 ILE cc_start: 0.9143 (tp) cc_final: 0.8875 (tp) outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.3018 time to fit residues: 19.1881 Evaluate side-chains 49 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 1.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3954 Z= 0.286 Angle : 0.563 9.264 5376 Z= 0.307 Chirality : 0.042 0.134 638 Planarity : 0.003 0.025 700 Dihedral : 4.569 22.065 547 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.30 % Favored : 90.29 % Rotamer: Outliers : 0.71 % Allowed : 20.99 % 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: -1.27 (0.36), residues: 484 helix: 1.49 (0.45), residues: 123 sheet: -1.18 (0.84), residues: 44 loop : -1.88 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 64 HIS 0.001 0.000 HIS C 128 PHE 0.009 0.001 PHE C 52 TYR 0.009 0.001 TYR F 97 ARG 0.003 0.000 ARG F 76 *********************** 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 49 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 107 MET cc_start: 0.9074 (tpp) cc_final: 0.8860 (tpp) REVERT: F 104 ILE cc_start: 0.9132 (tp) cc_final: 0.8866 (tp) outliers start: 3 outliers final: 3 residues processed: 47 average time/residue: 0.2901 time to fit residues: 17.9819 Evaluate side-chains 46 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 1.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3954 Z= 0.303 Angle : 0.578 9.927 5376 Z= 0.316 Chirality : 0.042 0.136 638 Planarity : 0.003 0.029 700 Dihedral : 4.575 22.052 547 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.62 % Allowed : 10.12 % Favored : 89.26 % Rotamer: Outliers : 0.94 % Allowed : 20.99 % Favored : 78.07 % 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: -1.30 (0.37), residues: 484 helix: 1.44 (0.45), residues: 123 sheet: -1.18 (0.84), residues: 44 loop : -1.90 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 64 HIS 0.001 0.000 HIS C 128 PHE 0.007 0.001 PHE C 52 TYR 0.009 0.001 TYR F 97 ARG 0.004 0.000 ARG F 76 ********************** 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 49 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 ILE cc_start: 0.9136 (mm) cc_final: 0.8817 (mt) REVERT: F 74 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8304 (tm-30) REVERT: F 104 ILE cc_start: 0.9138 (tp) cc_final: 0.8870 (tp) outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 0.2711 time to fit residues: 17.2506 Evaluate side-chains 47 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 2 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.079868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.071348 restraints weight = 38785.484| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.62 r_work: 0.3238 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 1.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3954 Z= 0.181 Angle : 0.542 10.304 5376 Z= 0.291 Chirality : 0.041 0.127 638 Planarity : 0.003 0.028 700 Dihedral : 4.363 21.534 547 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.68 % Favored : 90.70 % Rotamer: Outliers : 1.18 % Allowed : 20.75 % Favored : 78.07 % 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: -1.15 (0.37), residues: 484 helix: 1.61 (0.46), residues: 123 sheet: -1.14 (0.76), residues: 54 loop : -1.81 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 64 HIS 0.001 0.001 HIS E 108 PHE 0.007 0.001 PHE E 151 TYR 0.007 0.001 TYR F 97 ARG 0.003 0.000 ARG F 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3105.18 seconds wall clock time: 55 minutes 3.06 seconds (3303.06 seconds total)