Starting phenix.real_space_refine on Tue Feb 13 11:17:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saz_24959/02_2024/7saz_24959.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saz_24959/02_2024/7saz_24959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saz_24959/02_2024/7saz_24959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saz_24959/02_2024/7saz_24959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saz_24959/02_2024/7saz_24959.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saz_24959/02_2024/7saz_24959.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 3743 2.51 5 N 896 2.21 5 O 1044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B ASP 176": "OD1" <-> "OD2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ASP 207": "OD1" <-> "OD2" Residue "E TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 66": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5708 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1740 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 4, 'TRANS': 212} Chain: "B" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1723 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain: "C" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 472 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "D" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 456 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain: "F" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 442 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "G" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 442 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Time building chain proxies: 3.70, per 1000 atoms: 0.65 Number of scatterers: 5708 At special positions: 0 Unit cell: (68.224, 75.712, 114.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1044 8.00 N 896 7.00 C 3743 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 967.3 milliseconds 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1294 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 4 sheets defined 77.6% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 6 through 22 Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 28 through 67 removed outlier: 3.706A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 101 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.547A pdb=" N VAL A 112 " --> pdb=" O ASP A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 130 through 150 Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 183 through 190 Processing helix chain 'A' and resid 193 through 221 removed outlier: 3.712A pdb=" N LYS A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 29 removed outlier: 3.853A pdb=" N MET B 11 " --> pdb=" O PRO B 7 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU B 17 " --> pdb=" O ASN B 13 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 67 removed outlier: 3.673A pdb=" N GLY B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 101 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 132 through 152 removed outlier: 3.536A pdb=" N VAL B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.727A pdb=" N GLU B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 218 Processing helix chain 'C' and resid 8 through 33 removed outlier: 3.719A pdb=" N PHE C 12 " --> pdb=" O THR C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 65 removed outlier: 3.551A pdb=" N ALA C 64 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE C 65 " --> pdb=" O PHE C 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 33 Processing helix chain 'D' and resid 43 through 63 removed outlier: 4.080A pdb=" N PHE D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 48 " --> pdb=" O GLY D 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 33 Processing helix chain 'E' and resid 43 through 65 removed outlier: 4.010A pdb=" N PHE E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR E 55 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE E 65 " --> pdb=" O PHE E 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 33 removed outlier: 4.684A pdb=" N TYR F 16 " --> pdb=" O PHE F 12 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY F 17 " --> pdb=" O GLN F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 63 removed outlier: 3.959A pdb=" N PHE F 47 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU F 48 " --> pdb=" O GLY F 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 33 Processing helix chain 'G' and resid 43 through 64 removed outlier: 4.079A pdb=" N PHE G 47 " --> pdb=" O LEU G 43 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA3, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA4, first strand: chain 'B' and resid 174 through 175 434 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1786 1.34 - 1.46: 897 1.46 - 1.57: 3090 1.57 - 1.69: 0 1.69 - 1.80: 50 Bond restraints: 5823 Sorted by residual: bond pdb=" CG LEU B 42 " pdb=" CD2 LEU B 42 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.75e+00 bond pdb=" CG1 ILE D 59 " pdb=" CD1 ILE D 59 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.43e+00 bond pdb=" CG MET B 11 " pdb=" SD MET B 11 " ideal model delta sigma weight residual 1.803 1.769 0.034 2.50e-02 1.60e+03 1.84e+00 bond pdb=" CA GLY F 40 " pdb=" C GLY F 40 " ideal model delta sigma weight residual 1.514 1.531 -0.016 1.41e-02 5.03e+03 1.37e+00 bond pdb=" CG1 ILE F 59 " pdb=" CD1 ILE F 59 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.35e+00 ... (remaining 5818 not shown) Histogram of bond angle deviations from ideal: 95.98 - 103.57: 40 103.57 - 111.17: 2116 111.17 - 118.77: 2417 118.77 - 126.36: 3201 126.36 - 133.96: 42 Bond angle restraints: 7816 Sorted by residual: angle pdb=" N GLU B 47 " pdb=" CA GLU B 47 " pdb=" CB GLU B 47 " ideal model delta sigma weight residual 110.12 114.89 -4.77 1.47e+00 4.63e-01 1.05e+01 angle pdb=" CA MET B 11 " pdb=" CB MET B 11 " pdb=" CG MET B 11 " ideal model delta sigma weight residual 114.10 107.86 6.24 2.00e+00 2.50e-01 9.74e+00 angle pdb=" C MET A 113 " pdb=" N ASP A 114 " pdb=" CA ASP A 114 " ideal model delta sigma weight residual 121.54 127.11 -5.57 1.91e+00 2.74e-01 8.50e+00 angle pdb=" C THR A 157 " pdb=" N TYR A 158 " pdb=" CA TYR A 158 " ideal model delta sigma weight residual 121.54 127.01 -5.47 1.91e+00 2.74e-01 8.20e+00 angle pdb=" C ILE A 12 " pdb=" N ASN A 13 " pdb=" CA ASN A 13 " ideal model delta sigma weight residual 121.14 116.17 4.97 1.75e+00 3.27e-01 8.06e+00 ... (remaining 7811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 2962 15.25 - 30.50: 323 30.50 - 45.74: 90 45.74 - 60.99: 10 60.99 - 76.24: 6 Dihedral angle restraints: 3391 sinusoidal: 1355 harmonic: 2036 Sorted by residual: dihedral pdb=" CA MET A 113 " pdb=" C MET A 113 " pdb=" N ASP A 114 " pdb=" CA ASP A 114 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA TYR A 158 " pdb=" C TYR A 158 " pdb=" N GLY A 159 " pdb=" CA GLY A 159 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA PRO B 131 " pdb=" C PRO B 131 " pdb=" N GLU B 132 " pdb=" CA GLU B 132 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 3388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 665 0.050 - 0.101: 161 0.101 - 0.151: 12 0.151 - 0.202: 1 0.202 - 0.252: 1 Chirality restraints: 840 Sorted by residual: chirality pdb=" CG LEU B 42 " pdb=" CB LEU B 42 " pdb=" CD1 LEU B 42 " pdb=" CD2 LEU B 42 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ASP A 114 " pdb=" N ASP A 114 " pdb=" C ASP A 114 " pdb=" CB ASP A 114 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA PRO A 131 " pdb=" N PRO A 131 " pdb=" C PRO A 131 " pdb=" CB PRO A 131 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 837 not shown) Planarity restraints: 997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 130 " -0.052 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO B 131 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 131 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 131 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 130 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 131 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 66 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO C 67 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 67 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 67 " 0.017 5.00e-02 4.00e+02 ... (remaining 994 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 348 2.73 - 3.27: 6021 3.27 - 3.82: 9696 3.82 - 4.36: 11341 4.36 - 4.90: 19652 Nonbonded interactions: 47058 Sorted by model distance: nonbonded pdb=" OH TYR A 187 " pdb=" OE1 GLU B 30 " model vdw 2.188 2.440 nonbonded pdb=" NH2 ARG B 8 " pdb=" OE2 GLU C 56 " model vdw 2.237 2.520 nonbonded pdb=" ND2 ASN B 186 " pdb=" OE1 GLU B 190 " model vdw 2.285 2.520 nonbonded pdb=" O ILE F 59 " pdb=" OG SER F 63 " model vdw 2.287 2.440 nonbonded pdb=" OE1 GLU B 98 " pdb=" NZ LYS B 122 " model vdw 2.291 2.520 ... (remaining 47053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 220) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 10 through 65) selection = (chain 'D' and resid 10 through 65) selection = chain 'E' selection = (chain 'F' and resid 10 through 65) selection = (chain 'G' and resid 10 through 65) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.000 Extract box with map and model: 3.920 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 19.510 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.004 0.064 5823 Z= 0.271 Angle : 0.628 9.899 7816 Z= 0.354 Chirality : 0.041 0.252 840 Planarity : 0.004 0.077 997 Dihedral : 13.698 76.236 2097 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.67 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.31), residues: 708 helix: 1.14 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -3.14 (0.40), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 34 HIS 0.010 0.002 HIS G 33 PHE 0.013 0.001 PHE A 123 TYR 0.020 0.002 TYR B 216 ARG 0.015 0.001 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.675 Fit side-chains REVERT: A 173 ASP cc_start: 0.8789 (m-30) cc_final: 0.8425 (m-30) REVERT: B 100 MET cc_start: 0.8448 (mmp) cc_final: 0.8242 (mmt) REVERT: B 203 MET cc_start: 0.7223 (tpp) cc_final: 0.6960 (tpt) REVERT: B 207 ASP cc_start: 0.7846 (m-30) cc_final: 0.7641 (m-30) REVERT: C 10 LYS cc_start: 0.8166 (pptt) cc_final: 0.7060 (mptt) REVERT: D 14 MET cc_start: 0.8412 (ttm) cc_final: 0.8189 (ttp) REVERT: F 14 MET cc_start: 0.7609 (ttm) cc_final: 0.7184 (ttt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 1.1744 time to fit residues: 164.2681 Evaluate side-chains 94 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN B 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5823 Z= 0.182 Angle : 0.498 6.155 7816 Z= 0.276 Chirality : 0.038 0.220 840 Planarity : 0.003 0.047 997 Dihedral : 4.454 23.689 752 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.39 % Favored : 96.47 % Rotamer: Outliers : 2.89 % Allowed : 11.38 % Favored : 85.74 % 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: 1.17 (0.31), residues: 708 helix: 1.87 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -3.08 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 34 HIS 0.002 0.001 HIS G 33 PHE 0.011 0.001 PHE C 47 TYR 0.015 0.001 TYR E 16 ARG 0.001 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.602 Fit side-chains REVERT: A 13 ASN cc_start: 0.7403 (p0) cc_final: 0.6826 (m-40) REVERT: A 173 ASP cc_start: 0.8887 (m-30) cc_final: 0.8537 (m-30) REVERT: B 73 GLU cc_start: 0.7863 (pp20) cc_final: 0.7625 (tm-30) REVERT: B 100 MET cc_start: 0.8355 (mmp) cc_final: 0.7910 (mmt) REVERT: B 203 MET cc_start: 0.7201 (tpp) cc_final: 0.6704 (tpt) REVERT: B 207 ASP cc_start: 0.7837 (m-30) cc_final: 0.7496 (m-30) REVERT: D 14 MET cc_start: 0.8341 (ttm) cc_final: 0.8076 (ttp) REVERT: F 14 MET cc_start: 0.7544 (ttm) cc_final: 0.7326 (ttt) outliers start: 17 outliers final: 7 residues processed: 109 average time/residue: 1.1610 time to fit residues: 132.4484 Evaluate side-chains 97 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 42 optimal weight: 0.0170 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN A 170 ASN A 172 ASN B 172 ASN B 213 GLN G 33 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5823 Z= 0.187 Angle : 0.476 6.055 7816 Z= 0.263 Chirality : 0.037 0.205 840 Planarity : 0.003 0.038 997 Dihedral : 4.220 22.783 752 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.39 % Favored : 96.47 % Rotamer: Outliers : 2.38 % Allowed : 16.13 % Favored : 81.49 % 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: 1.48 (0.31), residues: 708 helix: 2.13 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -3.10 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 34 HIS 0.004 0.001 HIS G 33 PHE 0.009 0.001 PHE D 60 TYR 0.015 0.001 TYR E 16 ARG 0.002 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7223 (p0) cc_final: 0.6855 (m-40) REVERT: A 61 GLU cc_start: 0.7432 (tp30) cc_final: 0.7080 (tm-30) REVERT: A 170 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7577 (m-40) REVERT: A 173 ASP cc_start: 0.8849 (m-30) cc_final: 0.8470 (m-30) REVERT: B 100 MET cc_start: 0.8335 (mmp) cc_final: 0.7906 (mmt) outliers start: 14 outliers final: 5 residues processed: 103 average time/residue: 1.1410 time to fit residues: 123.2635 Evaluate side-chains 94 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 65 optimal weight: 0.0970 chunk 58 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN A 170 ASN B 172 ASN B 213 GLN D 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5823 Z= 0.208 Angle : 0.483 7.464 7816 Z= 0.262 Chirality : 0.038 0.270 840 Planarity : 0.003 0.037 997 Dihedral : 4.167 22.622 752 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.11 % Favored : 96.75 % Rotamer: Outliers : 3.23 % Allowed : 17.66 % Favored : 79.12 % 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: 1.59 (0.31), residues: 708 helix: 2.22 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -3.13 (0.40), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 184 HIS 0.004 0.001 HIS G 33 PHE 0.010 0.001 PHE A 169 TYR 0.017 0.001 TYR E 16 ARG 0.002 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7210 (p0) cc_final: 0.6878 (m-40) REVERT: A 105 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6923 (tm-30) REVERT: A 173 ASP cc_start: 0.8757 (m-30) cc_final: 0.8542 (m-30) REVERT: A 219 MET cc_start: 0.7641 (mmp) cc_final: 0.7014 (mtp) REVERT: B 73 GLU cc_start: 0.7820 (pp20) cc_final: 0.7490 (tm-30) REVERT: B 100 MET cc_start: 0.8337 (mmp) cc_final: 0.8071 (mmp) REVERT: B 102 GLN cc_start: 0.8365 (pp30) cc_final: 0.7298 (pp30) outliers start: 19 outliers final: 9 residues processed: 103 average time/residue: 1.0909 time to fit residues: 118.0002 Evaluate side-chains 97 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN B 172 ASN B 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5823 Z= 0.206 Angle : 0.477 7.042 7816 Z= 0.261 Chirality : 0.038 0.270 840 Planarity : 0.003 0.038 997 Dihedral : 4.117 22.752 752 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.39 % Favored : 96.47 % Rotamer: Outliers : 2.55 % Allowed : 18.34 % Favored : 79.12 % 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: 1.68 (0.31), residues: 708 helix: 2.27 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -3.03 (0.41), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 184 HIS 0.003 0.001 HIS G 33 PHE 0.009 0.001 PHE D 60 TYR 0.016 0.001 TYR E 16 ARG 0.002 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7057 (p0) cc_final: 0.6786 (m-40) REVERT: A 105 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: A 173 ASP cc_start: 0.8847 (m-30) cc_final: 0.8615 (m-30) REVERT: A 219 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7234 (mtp) REVERT: B 73 GLU cc_start: 0.7815 (pp20) cc_final: 0.7511 (tm-30) REVERT: B 102 GLN cc_start: 0.8360 (pp30) cc_final: 0.7335 (pp30) outliers start: 15 outliers final: 10 residues processed: 101 average time/residue: 1.0827 time to fit residues: 114.8436 Evaluate side-chains 101 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN A 141 ASN B 172 ASN B 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5823 Z= 0.269 Angle : 0.514 8.310 7816 Z= 0.277 Chirality : 0.040 0.341 840 Planarity : 0.003 0.037 997 Dihedral : 4.188 22.023 752 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.81 % Favored : 96.05 % Rotamer: Outliers : 3.40 % Allowed : 19.19 % Favored : 77.42 % 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: 1.58 (0.31), residues: 708 helix: 2.18 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -3.00 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 184 HIS 0.003 0.001 HIS G 33 PHE 0.010 0.001 PHE D 60 TYR 0.017 0.001 TYR E 16 ARG 0.002 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7249 (p0) cc_final: 0.6779 (m-40) REVERT: A 58 GLN cc_start: 0.7375 (mt0) cc_final: 0.6994 (mt0) REVERT: A 61 GLU cc_start: 0.7640 (tp30) cc_final: 0.7090 (tm-30) REVERT: A 105 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6898 (tm-30) REVERT: A 173 ASP cc_start: 0.8846 (m-30) cc_final: 0.8604 (m-30) REVERT: A 219 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7174 (mtp) REVERT: B 73 GLU cc_start: 0.7824 (pp20) cc_final: 0.7431 (tm-30) REVERT: B 79 LYS cc_start: 0.8429 (mtpt) cc_final: 0.8138 (mtpp) REVERT: B 102 GLN cc_start: 0.8351 (pp30) cc_final: 0.7330 (pp30) outliers start: 20 outliers final: 12 residues processed: 103 average time/residue: 1.0982 time to fit residues: 118.9655 Evaluate side-chains 102 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 172 ASN B 172 ASN B 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5823 Z= 0.173 Angle : 0.475 8.190 7816 Z= 0.259 Chirality : 0.039 0.316 840 Planarity : 0.003 0.038 997 Dihedral : 4.058 23.001 752 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.11 % Favored : 96.75 % Rotamer: Outliers : 3.23 % Allowed : 19.52 % Favored : 77.25 % 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: 1.79 (0.31), residues: 708 helix: 2.34 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -2.95 (0.41), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 34 HIS 0.004 0.001 HIS G 33 PHE 0.009 0.001 PHE D 60 TYR 0.016 0.001 TYR E 16 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7025 (p0) cc_final: 0.6661 (m-40) REVERT: A 58 GLN cc_start: 0.7463 (mt0) cc_final: 0.7096 (mt0) REVERT: A 61 GLU cc_start: 0.7514 (tp30) cc_final: 0.7035 (tm-30) REVERT: A 105 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6875 (tm-30) REVERT: A 173 ASP cc_start: 0.8841 (m-30) cc_final: 0.8439 (m-30) REVERT: B 73 GLU cc_start: 0.7821 (pp20) cc_final: 0.7496 (tm-30) REVERT: B 79 LYS cc_start: 0.8439 (mtpt) cc_final: 0.8146 (mtpp) REVERT: B 102 GLN cc_start: 0.8307 (pp30) cc_final: 0.7332 (pp30) REVERT: C 48 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8521 (mt) outliers start: 19 outliers final: 12 residues processed: 105 average time/residue: 1.1637 time to fit residues: 128.0530 Evaluate side-chains 104 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 0.0010 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 36 optimal weight: 9.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 172 ASN B 62 GLN B 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5823 Z= 0.170 Angle : 0.489 13.052 7816 Z= 0.262 Chirality : 0.040 0.417 840 Planarity : 0.003 0.038 997 Dihedral : 3.963 22.485 752 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.25 % Favored : 96.61 % Rotamer: Outliers : 3.06 % Allowed : 20.71 % Favored : 76.23 % 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: 1.86 (0.31), residues: 708 helix: 2.39 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -2.88 (0.42), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 34 HIS 0.004 0.001 HIS G 33 PHE 0.010 0.001 PHE D 60 TYR 0.015 0.001 TYR E 16 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7049 (p0) cc_final: 0.6635 (m-40) REVERT: A 58 GLN cc_start: 0.7464 (mt0) cc_final: 0.7234 (mt0) REVERT: A 61 GLU cc_start: 0.7462 (tp30) cc_final: 0.7003 (tm-30) REVERT: A 105 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6875 (tm-30) REVERT: A 111 GLN cc_start: 0.7834 (tt0) cc_final: 0.7578 (pt0) REVERT: A 173 ASP cc_start: 0.8826 (m-30) cc_final: 0.8557 (m-30) REVERT: B 73 GLU cc_start: 0.7815 (pp20) cc_final: 0.7492 (tm-30) REVERT: B 79 LYS cc_start: 0.8434 (mtpt) cc_final: 0.8132 (mtpp) REVERT: B 102 GLN cc_start: 0.8272 (pp30) cc_final: 0.7231 (pp30) REVERT: C 48 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8540 (mt) outliers start: 18 outliers final: 8 residues processed: 103 average time/residue: 1.1341 time to fit residues: 122.5922 Evaluate side-chains 100 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 55 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.0970 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.6336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5823 Z= 0.158 Angle : 0.487 13.310 7816 Z= 0.261 Chirality : 0.040 0.443 840 Planarity : 0.003 0.039 997 Dihedral : 3.928 22.739 752 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.97 % Favored : 96.89 % Rotamer: Outliers : 2.55 % Allowed : 21.22 % Favored : 76.23 % 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: 1.93 (0.32), residues: 708 helix: 2.47 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -2.90 (0.42), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 34 HIS 0.004 0.001 HIS G 33 PHE 0.010 0.001 PHE D 60 TYR 0.016 0.001 TYR B 89 ARG 0.003 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.6991 (p0) cc_final: 0.6663 (m-40) REVERT: A 58 GLN cc_start: 0.7466 (mt0) cc_final: 0.7128 (mt0) REVERT: A 61 GLU cc_start: 0.7494 (tp30) cc_final: 0.7052 (tm-30) REVERT: A 105 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: A 111 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7679 (pt0) REVERT: A 173 ASP cc_start: 0.8802 (m-30) cc_final: 0.8529 (m-30) REVERT: B 73 GLU cc_start: 0.7763 (pp20) cc_final: 0.7473 (tm-30) REVERT: B 79 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8108 (mtpp) REVERT: B 102 GLN cc_start: 0.8247 (pp30) cc_final: 0.7215 (pp30) REVERT: C 48 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8526 (mt) outliers start: 15 outliers final: 9 residues processed: 102 average time/residue: 1.1349 time to fit residues: 121.3625 Evaluate side-chains 105 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5823 Z= 0.217 Angle : 0.515 12.940 7816 Z= 0.274 Chirality : 0.041 0.454 840 Planarity : 0.003 0.041 997 Dihedral : 3.983 22.240 752 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.25 % Favored : 96.61 % Rotamer: Outliers : 2.21 % Allowed : 22.24 % Favored : 75.55 % 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: 1.80 (0.31), residues: 708 helix: 2.35 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -2.87 (0.42), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 184 HIS 0.003 0.001 HIS G 33 PHE 0.010 0.001 PHE D 60 TYR 0.020 0.001 TYR B 89 ARG 0.003 0.000 ARG A 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7107 (p0) cc_final: 0.6702 (m-40) REVERT: A 105 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: A 111 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7744 (pt0) REVERT: A 173 ASP cc_start: 0.8849 (m-30) cc_final: 0.8573 (m-30) REVERT: B 73 GLU cc_start: 0.7772 (pp20) cc_final: 0.7489 (tm-30) REVERT: B 79 LYS cc_start: 0.8424 (mtpt) cc_final: 0.8100 (mtpp) REVERT: B 102 GLN cc_start: 0.8271 (pp30) cc_final: 0.7227 (pp30) REVERT: C 48 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8510 (mt) outliers start: 13 outliers final: 9 residues processed: 99 average time/residue: 1.2401 time to fit residues: 128.5061 Evaluate side-chains 104 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 36 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 172 ASN B 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.113496 restraints weight = 6749.087| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.24 r_work: 0.3136 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5823 Z= 0.154 Angle : 0.485 13.431 7816 Z= 0.260 Chirality : 0.040 0.444 840 Planarity : 0.003 0.044 997 Dihedral : 3.874 22.883 752 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.82 % Favored : 97.03 % Rotamer: Outliers : 2.21 % Allowed : 22.24 % Favored : 75.55 % 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 (0.32), residues: 708 helix: 2.46 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -2.86 (0.42), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 34 HIS 0.004 0.001 HIS G 33 PHE 0.011 0.001 PHE D 60 TYR 0.018 0.001 TYR E 16 ARG 0.003 0.000 ARG A 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2532.17 seconds wall clock time: 45 minutes 33.77 seconds (2733.77 seconds total)