Starting phenix.real_space_refine on Tue Feb 13 10:42:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlk_22246/02_2024/6xlk_22246_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlk_22246/02_2024/6xlk_22246.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/6xlk_22246/02_2024/6xlk_22246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlk_22246/02_2024/6xlk_22246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlk_22246/02_2024/6xlk_22246_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlk_22246/02_2024/6xlk_22246_updated.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= 0.004 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: 6 Type Number sf(0) Gaussians Sb 2 10.97 5 P 44 5.49 5 S 26 5.16 5 C 3386 2.51 5 N 912 2.21 5 O 1086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 79": "OE1" <-> "OE2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "G ARG 90": "NH1" <-> "NH2" Residue "G TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 135": "OD1" <-> "OD2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "G ASP 189": "OD1" <-> "OD2" Residue "G GLU 194": "OE1" <-> "OE2" Residue "G TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 257": "OE1" <-> "OE2" Residue "H ASP 35": "OD1" <-> "OD2" Residue "H ARG 56": "NH1" <-> "NH2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "H ARG 81": "NH1" <-> "NH2" Residue "H ASP 94": "OD1" <-> "OD2" Residue "H GLU 120": "OE1" <-> "OE2" Residue "H PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 173": "OE1" <-> "OE2" Residue "H ASP 189": "OD1" <-> "OD2" Residue "H GLU 194": "OE1" <-> "OE2" Residue "H ARG 220": "NH1" <-> "NH2" Residue "H ASP 247": "OD1" <-> "OD2" Residue "H GLU 267": "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: 5456 Number of models: 1 Model: "" Number of chains: 6 Chain: "N" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "T" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 467 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "G" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "H" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'118': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'118': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 3.75, per 1000 atoms: 0.69 Number of scatterers: 5456 At special positions: 0 Unit cell: (86.645, 115.971, 87.978, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Sb 2 50.95 S 26 16.00 P 44 15.00 O 1086 8.00 N 912 7.00 C 3386 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: 2.44 Conformation dependent library (CDL) restraints added in 915.9 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1028 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 4 sheets defined 41.2% alpha, 19.8% beta 23 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'G' and resid 4 through 11 Processing helix chain 'G' and resid 15 through 23 Processing helix chain 'G' and resid 43 through 58 removed outlier: 3.941A pdb=" N LYS G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN G 51 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 70 Processing helix chain 'G' and resid 75 through 108 Processing helix chain 'G' and resid 136 through 141 removed outlier: 3.952A pdb=" N LYS G 141 " --> pdb=" O SER G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 153 removed outlier: 3.633A pdb=" N MET G 151 " --> pdb=" O GLY G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 232 removed outlier: 4.799A pdb=" N ARG G 220 " --> pdb=" O ASP G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 10 Processing helix chain 'H' and resid 15 through 24 Processing helix chain 'H' and resid 43 through 58 removed outlier: 3.540A pdb=" N GLN H 51 " --> pdb=" O MET H 47 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU H 58 " --> pdb=" O SER H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 76 through 108 removed outlier: 3.551A pdb=" N ARG H 81 " --> pdb=" O ILE H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 153 Proline residue: H 144 - end of helix Processing helix chain 'H' and resid 216 through 232 removed outlier: 4.960A pdb=" N ARG H 220 " --> pdb=" O ASP H 217 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN H 221 " --> pdb=" O SER H 218 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP H 232 " --> pdb=" O TRP H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing sheet with id= A, first strand: chain 'G' and resid 117 through 121 removed outlier: 6.703A pdb=" N GLU G 261 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYR G 245 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLN G 263 " --> pdb=" O GLU G 243 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLU G 243 " --> pdb=" O GLN G 263 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N CYS G 165 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE G 125 " --> pdb=" O VAL G 187 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 235 through 237 Processing sheet with id= C, first strand: chain 'H' and resid 117 through 121 removed outlier: 6.403A pdb=" N GLU H 261 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N TYR H 245 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN H 263 " --> pdb=" O GLU H 243 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU H 243 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N CYS H 165 " --> pdb=" O TYR H 245 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 235 through 237 222 hydrogen bonds defined for protein. 561 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 2323 1.39 - 1.58: 3224 1.58 - 1.76: 88 1.76 - 1.95: 42 1.95 - 2.13: 8 Bond restraints: 5685 Sorted by residual: bond pdb="SB 118 H 302 " pdb=" C1C 118 H 302 " ideal model delta sigma weight residual 2.092 2.132 -0.040 2.00e-02 2.50e+03 4.04e+00 bond pdb="SB 118 G 302 " pdb=" C1C 118 G 302 " ideal model delta sigma weight residual 2.092 2.132 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb="SB 118 G 302 " pdb=" C1D 118 G 302 " ideal model delta sigma weight residual 2.092 2.129 -0.037 2.00e-02 2.50e+03 3.51e+00 bond pdb="SB 118 H 302 " pdb=" C1D 118 H 302 " ideal model delta sigma weight residual 2.092 2.128 -0.036 2.00e-02 2.50e+03 3.32e+00 bond pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.11e+00 ... (remaining 5680 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.47: 431 106.47 - 113.36: 3098 113.36 - 120.24: 2179 120.24 - 127.13: 2063 127.13 - 134.02: 137 Bond angle restraints: 7908 Sorted by residual: angle pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " pdb=" P DT N 62 " ideal model delta sigma weight residual 120.20 124.66 -4.46 1.50e+00 4.44e-01 8.85e+00 angle pdb=" N PRO H 144 " pdb=" CA PRO H 144 " pdb=" C PRO H 144 " ideal model delta sigma weight residual 110.70 113.79 -3.09 1.22e+00 6.72e-01 6.44e+00 angle pdb=" CA TYR H 127 " pdb=" CB TYR H 127 " pdb=" CG TYR H 127 " ideal model delta sigma weight residual 113.90 118.39 -4.49 1.80e+00 3.09e-01 6.22e+00 angle pdb=" C4' DG T 40 " pdb=" O4' DG T 40 " pdb=" C1' DG T 40 " ideal model delta sigma weight residual 109.70 105.97 3.73 1.50e+00 4.44e-01 6.17e+00 angle pdb=" C THR G 206 " pdb=" CA THR G 206 " pdb=" CB THR G 206 " ideal model delta sigma weight residual 109.80 113.58 -3.78 1.64e+00 3.72e-01 5.31e+00 ... (remaining 7903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.85: 3077 31.85 - 63.70: 276 63.70 - 95.54: 13 95.54 - 127.39: 2 127.39 - 159.24: 1 Dihedral angle restraints: 3369 sinusoidal: 1773 harmonic: 1596 Sorted by residual: dihedral pdb=" C23 1N7 H 301 " pdb=" C20 1N7 H 301 " pdb=" C22 1N7 H 301 " pdb=" C9 1N7 H 301 " ideal model delta sinusoidal sigma weight residual 155.16 -89.44 -115.40 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C4' DT N 61 " pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " pdb=" P DT N 62 " ideal model delta sinusoidal sigma weight residual 220.00 60.76 159.24 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" CA VAL H 126 " pdb=" C VAL H 126 " pdb=" N TYR H 127 " pdb=" CA TYR H 127 " ideal model delta harmonic sigma weight residual 180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 3366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 639 0.050 - 0.100: 190 0.100 - 0.150: 36 0.150 - 0.199: 7 0.199 - 0.249: 4 Chirality restraints: 876 Sorted by residual: chirality pdb=" CB ILE H 125 " pdb=" CA ILE H 125 " pdb=" CG1 ILE H 125 " pdb=" CG2 ILE H 125 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C6 1N7 H 301 " pdb=" C18 1N7 H 301 " pdb=" C5 1N7 H 301 " pdb=" C7 1N7 H 301 " both_signs ideal model delta sigma weight residual False -2.43 -2.63 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C13 1N7 G 301 " pdb=" C12 1N7 G 301 " pdb=" C14 1N7 G 301 " pdb=" O2 1N7 G 301 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 873 not shown) Planarity restraints: 832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO G 144 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.21e+00 pdb=" N PRO G 145 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO G 145 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 145 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 224 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C ILE G 224 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE G 224 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR G 225 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 206 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C THR G 206 " 0.026 2.00e-02 2.50e+03 pdb=" O THR G 206 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA G 207 " -0.009 2.00e-02 2.50e+03 ... (remaining 829 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 833 2.75 - 3.29: 5125 3.29 - 3.83: 9686 3.83 - 4.36: 11493 4.36 - 4.90: 18303 Nonbonded interactions: 45440 Sorted by model distance: nonbonded pdb=" NE2 HIS G 170 " pdb=" OE1 GLU G 182 " model vdw 2.216 2.520 nonbonded pdb=" OG1 THR G 61 " pdb=" OE1 GLU G 64 " model vdw 2.233 2.440 nonbonded pdb=" OH TYR G 139 " pdb=" OG1 THR G 167 " model vdw 2.245 2.440 nonbonded pdb=" OH TYR G 127 " pdb=" OE1 GLU G 185 " model vdw 2.250 2.440 nonbonded pdb=" OG SER H 2 " pdb=" O TYR H 41 " model vdw 2.266 2.440 ... (remaining 45435 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 'G' selection = (chain 'H' and (resid 2 through 269 or (resid 301 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 o \ r name O2 or name O3 or name O4 )) or resid 302)) } ncs_group { reference = (chain 'N' and (resid 41 through 50 or resid 52 through 61)) selection = (chain 'T' and (resid 28 through 37 or resid 39 through 48)) } 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: 0.730 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: 3.850 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 20.950 Find NCS groups from input model: 0.240 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.008 0.054 5685 Z= 0.500 Angle : 0.756 7.684 7908 Z= 0.424 Chirality : 0.050 0.249 876 Planarity : 0.004 0.057 832 Dihedral : 20.173 159.238 2341 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.41 % Allowed : 9.80 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.26 (0.31), residues: 532 helix: -0.90 (0.30), residues: 222 sheet: -2.49 (0.42), residues: 102 loop : -1.40 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 229 HIS 0.006 0.001 HIS G 105 PHE 0.013 0.002 PHE H 190 TYR 0.024 0.002 TYR H 127 ARG 0.005 0.001 ARG G 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.576 Fit side-chains REVERT: H 92 MET cc_start: 0.8307 (mmt) cc_final: 0.7896 (mmt) REVERT: H 259 MET cc_start: 0.8157 (ttp) cc_final: 0.7952 (ttm) outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 0.2770 time to fit residues: 18.5644 Evaluate side-chains 38 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.0370 chunk 50 optimal weight: 0.0670 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 45 GLN G 51 GLN G 76 HIS G 105 HIS G 148 GLN H 3 GLN H 50 HIS H 154 ASN H 193 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5685 Z= 0.165 Angle : 0.500 7.346 7908 Z= 0.287 Chirality : 0.038 0.179 876 Planarity : 0.004 0.052 832 Dihedral : 20.636 158.610 1230 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.04 % Allowed : 11.43 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.77 (0.34), residues: 532 helix: 0.49 (0.34), residues: 222 sheet: -2.17 (0.47), residues: 92 loop : -0.62 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 229 HIS 0.002 0.001 HIS H 50 PHE 0.009 0.001 PHE H 190 TYR 0.016 0.001 TYR H 127 ARG 0.005 0.000 ARG H 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: G 259 MET cc_start: 0.8149 (ttm) cc_final: 0.7856 (ttm) REVERT: H 92 MET cc_start: 0.8263 (mmt) cc_final: 0.7742 (mmt) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.1718 time to fit residues: 13.2182 Evaluate side-chains 45 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 266 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 0.0040 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- 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: 0.8131 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5685 Z= 0.213 Angle : 0.504 7.299 7908 Z= 0.287 Chirality : 0.038 0.145 876 Planarity : 0.004 0.048 832 Dihedral : 20.504 157.773 1230 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.84 % Allowed : 14.69 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.18 (0.35), residues: 532 helix: 1.03 (0.34), residues: 222 sheet: -2.00 (0.48), residues: 92 loop : -0.29 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 229 HIS 0.007 0.001 HIS G 105 PHE 0.015 0.001 PHE G 264 TYR 0.019 0.001 TYR H 127 ARG 0.003 0.000 ARG G 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.501 Fit side-chains REVERT: G 227 MET cc_start: 0.8465 (mmm) cc_final: 0.8171 (mmm) REVERT: G 259 MET cc_start: 0.8176 (ttm) cc_final: 0.7845 (ttm) REVERT: H 92 MET cc_start: 0.8478 (mmt) cc_final: 0.7886 (mmt) outliers start: 9 outliers final: 8 residues processed: 46 average time/residue: 0.1242 time to fit residues: 8.6166 Evaluate side-chains 40 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 266 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 HIS H 105 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5685 Z= 0.205 Angle : 0.492 6.875 7908 Z= 0.282 Chirality : 0.038 0.144 876 Planarity : 0.004 0.047 832 Dihedral : 20.461 157.540 1228 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.04 % Allowed : 15.31 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.01 (0.36), residues: 532 helix: 1.21 (0.34), residues: 228 sheet: -1.96 (0.46), residues: 102 loop : -0.15 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 229 HIS 0.003 0.001 HIS G 105 PHE 0.013 0.001 PHE G 264 TYR 0.018 0.001 TYR H 127 ARG 0.003 0.000 ARG H 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.575 Fit side-chains REVERT: G 259 MET cc_start: 0.8164 (ttm) cc_final: 0.7799 (ttm) REVERT: H 92 MET cc_start: 0.8535 (mmt) cc_final: 0.7966 (mmt) outliers start: 10 outliers final: 9 residues processed: 48 average time/residue: 0.1408 time to fit residues: 9.9024 Evaluate side-chains 44 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 266 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8129 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5685 Z= 0.209 Angle : 0.492 7.366 7908 Z= 0.280 Chirality : 0.038 0.140 876 Planarity : 0.004 0.045 832 Dihedral : 20.464 157.345 1228 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.65 % Allowed : 15.10 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.36), residues: 532 helix: 1.44 (0.34), residues: 228 sheet: -1.93 (0.46), residues: 102 loop : -0.03 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 229 HIS 0.002 0.001 HIS G 50 PHE 0.011 0.001 PHE G 264 TYR 0.017 0.001 TYR H 127 ARG 0.002 0.000 ARG H 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 34 time to evaluate : 0.584 Fit side-chains REVERT: G 151 MET cc_start: 0.7925 (mmm) cc_final: 0.7655 (mmt) REVERT: G 227 MET cc_start: 0.8438 (mmm) cc_final: 0.8169 (mmm) REVERT: G 259 MET cc_start: 0.8208 (ttm) cc_final: 0.7828 (ttm) REVERT: H 92 MET cc_start: 0.8504 (mmt) cc_final: 0.8077 (mmt) outliers start: 13 outliers final: 10 residues processed: 46 average time/residue: 0.1277 time to fit residues: 8.8353 Evaluate side-chains 42 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 266 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8112 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5685 Z= 0.174 Angle : 0.473 6.693 7908 Z= 0.271 Chirality : 0.037 0.139 876 Planarity : 0.004 0.044 832 Dihedral : 20.349 156.965 1228 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.65 % Allowed : 14.90 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.42 (0.36), residues: 532 helix: 1.62 (0.34), residues: 228 sheet: -1.89 (0.46), residues: 102 loop : 0.09 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 229 HIS 0.002 0.000 HIS G 50 PHE 0.010 0.001 PHE G 264 TYR 0.015 0.001 TYR H 127 ARG 0.002 0.000 ARG G 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 36 time to evaluate : 0.576 Fit side-chains REVERT: G 259 MET cc_start: 0.8203 (ttm) cc_final: 0.7802 (ttm) REVERT: H 92 MET cc_start: 0.8469 (mmt) cc_final: 0.8086 (mmt) outliers start: 13 outliers final: 11 residues processed: 49 average time/residue: 0.1150 time to fit residues: 8.7905 Evaluate side-chains 43 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 167 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8118 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5685 Z= 0.199 Angle : 0.505 10.357 7908 Z= 0.280 Chirality : 0.038 0.141 876 Planarity : 0.004 0.043 832 Dihedral : 20.385 156.789 1228 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.65 % Allowed : 15.31 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.51 (0.36), residues: 532 helix: 1.70 (0.34), residues: 228 sheet: -1.87 (0.46), residues: 102 loop : 0.16 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 229 HIS 0.002 0.001 HIS G 50 PHE 0.009 0.001 PHE G 264 TYR 0.016 0.001 TYR H 127 ARG 0.002 0.000 ARG G 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 31 time to evaluate : 0.568 Fit side-chains REVERT: G 259 MET cc_start: 0.8222 (ttm) cc_final: 0.7813 (ttm) REVERT: H 92 MET cc_start: 0.8472 (mmt) cc_final: 0.8088 (mmt) REVERT: H 189 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7890 (p0) outliers start: 13 outliers final: 11 residues processed: 44 average time/residue: 0.1127 time to fit residues: 7.7297 Evaluate side-chains 40 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 28 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 189 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 0.0470 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 233 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5685 Z= 0.195 Angle : 0.482 6.759 7908 Z= 0.275 Chirality : 0.038 0.138 876 Planarity : 0.004 0.045 832 Dihedral : 20.382 156.787 1228 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.86 % Allowed : 14.90 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.55 (0.37), residues: 532 helix: 1.75 (0.34), residues: 228 sheet: -1.86 (0.52), residues: 90 loop : -0.01 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 229 HIS 0.002 0.001 HIS G 50 PHE 0.006 0.001 PHE G 264 TYR 0.016 0.001 TYR H 127 ARG 0.002 0.000 ARG G 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 31 time to evaluate : 0.567 Fit side-chains REVERT: G 259 MET cc_start: 0.8296 (ttm) cc_final: 0.7826 (ttm) REVERT: H 92 MET cc_start: 0.8466 (mmt) cc_final: 0.8083 (mmt) outliers start: 14 outliers final: 12 residues processed: 45 average time/residue: 0.1095 time to fit residues: 7.7400 Evaluate side-chains 41 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 29 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 167 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.5980 chunk 47 optimal weight: 0.0030 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 0.0020 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 0.0010 overall best weight: 0.1404 ------------------------------------------------------------------------------- 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: 0.8052 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5685 Z= 0.144 Angle : 0.496 10.668 7908 Z= 0.274 Chirality : 0.037 0.163 876 Planarity : 0.003 0.043 832 Dihedral : 20.035 155.712 1228 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.45 % Allowed : 14.90 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.62 (0.37), residues: 532 helix: 1.75 (0.35), residues: 234 sheet: -1.79 (0.47), residues: 102 loop : 0.20 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 258 HIS 0.001 0.000 HIS H 212 PHE 0.008 0.001 PHE G 264 TYR 0.012 0.001 TYR H 127 ARG 0.002 0.000 ARG H 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.524 Fit side-chains REVERT: G 151 MET cc_start: 0.7417 (mmm) cc_final: 0.7170 (mmt) REVERT: G 259 MET cc_start: 0.8195 (ttm) cc_final: 0.7811 (ttm) REVERT: H 92 MET cc_start: 0.8402 (mmt) cc_final: 0.8068 (mmt) outliers start: 12 outliers final: 10 residues processed: 52 average time/residue: 0.1068 time to fit residues: 8.5575 Evaluate side-chains 44 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 34 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 167 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 6 optimal weight: 0.0370 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 233 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5685 Z= 0.185 Angle : 0.502 9.930 7908 Z= 0.280 Chirality : 0.038 0.163 876 Planarity : 0.003 0.042 832 Dihedral : 20.207 155.427 1228 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.04 % Allowed : 15.92 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.58 (0.37), residues: 532 helix: 1.75 (0.34), residues: 236 sheet: -1.66 (0.48), residues: 100 loop : -0.02 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 229 HIS 0.002 0.001 HIS G 50 PHE 0.010 0.001 PHE G 264 TYR 0.014 0.001 TYR H 127 ARG 0.003 0.000 ARG H 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.547 Fit side-chains REVERT: G 151 MET cc_start: 0.7541 (mmm) cc_final: 0.7297 (mmt) REVERT: G 259 MET cc_start: 0.8279 (ttm) cc_final: 0.7969 (ttm) REVERT: H 92 MET cc_start: 0.8445 (mmt) cc_final: 0.8102 (mmt) outliers start: 10 outliers final: 9 residues processed: 42 average time/residue: 0.1180 time to fit residues: 7.7243 Evaluate side-chains 41 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 167 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 233 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.103901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.090082 restraints weight = 7743.635| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.58 r_work: 0.3262 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5685 Z= 0.211 Angle : 0.512 9.643 7908 Z= 0.285 Chirality : 0.038 0.150 876 Planarity : 0.003 0.042 832 Dihedral : 20.338 156.422 1228 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.04 % Allowed : 15.92 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.64 (0.37), residues: 532 helix: 1.72 (0.34), residues: 236 sheet: -1.70 (0.44), residues: 114 loop : 0.36 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 229 HIS 0.002 0.001 HIS G 50 PHE 0.009 0.001 PHE G 264 TYR 0.016 0.001 TYR H 127 ARG 0.003 0.000 ARG H 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1369.37 seconds wall clock time: 25 minutes 36.87 seconds (1536.87 seconds total)