Starting phenix.real_space_refine on Sun Mar 10 22:25:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fci_31526/03_2024/7fci_31526.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fci_31526/03_2024/7fci_31526.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/7fci_31526/03_2024/7fci_31526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fci_31526/03_2024/7fci_31526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fci_31526/03_2024/7fci_31526.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fci_31526/03_2024/7fci_31526.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= 0.003 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 47 5.16 5 C 3622 2.51 5 N 899 2.21 5 O 1045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 147": "OD1" <-> "OD2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 78": "OE1" <-> "OE2" Residue "L TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 102": "OD1" <-> "OD2" Residue "H TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5613 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2280 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain: "L" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1640 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 202} Chain: "H" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1693 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 208} Time building chain proxies: 3.35, per 1000 atoms: 0.60 Number of scatterers: 5613 At special positions: 0 Unit cell: (57.201, 66.32, 135.127, 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 47 16.00 O 1045 8.00 N 899 7.00 C 3622 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 204 " distance=2.03 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: 2.03 Conformation dependent library (CDL) restraints added in 1.1 seconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1362 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 41.4% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 20 through 43 removed outlier: 3.900A pdb=" N ASP A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.544A pdb=" N LYS A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 103 through 112 Processing helix chain 'A' and resid 115 through 143 removed outlier: 3.569A pdb=" N ILE A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 155 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 180 through 216 removed outlier: 3.824A pdb=" N MET A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG A 185 " --> pdb=" O PRO A 181 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.689A pdb=" N ARG A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 310 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.566A pdb=" N ASP L 81 " --> pdb=" O GLU L 78 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 82' Processing helix chain 'L' and resid 120 through 127 Processing helix chain 'L' and resid 182 through 188 removed outlier: 3.775A pdb=" N HIS L 188 " --> pdb=" O GLU L 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.057A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.529A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'H' and resid 195 through 200 Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.778A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.620A pdb=" N THR L 96 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 115 through 117 removed outlier: 3.852A pdb=" N VAL L 132 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR L 172 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA7, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.597A pdb=" N GLU H 10 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR H 119 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.597A pdb=" N GLU H 10 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR H 119 " --> pdb=" O GLU H 10 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.703A pdb=" N GLY H 148 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N CYS H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER H 188 " --> pdb=" O CYS H 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 160 through 163 Processing sheet with id=AB2, first strand: chain 'H' and resid 178 through 180 331 hydrogen bonds defined for protein. 915 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: 1.73 Time building geometry restraints manager: 2.27 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: 1549 1.34 - 1.45: 1038 1.45 - 1.57: 3090 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 5749 Sorted by residual: bond pdb=" CB PRO A 220 " pdb=" CG PRO A 220 " ideal model delta sigma weight residual 1.492 1.558 -0.066 5.00e-02 4.00e+02 1.73e+00 bond pdb=" CB GLU A 257 " pdb=" CG GLU A 257 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" CG PRO L 94 " pdb=" CD PRO L 94 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.09e+00 bond pdb=" CA VAL H 159 " pdb=" CB VAL H 159 " ideal model delta sigma weight residual 1.551 1.540 0.011 1.08e-02 8.57e+03 9.47e-01 bond pdb=" CA VAL H 106 " pdb=" CB VAL H 106 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.47e-02 4.63e+03 9.15e-01 ... (remaining 5744 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.29: 190 106.29 - 113.23: 3167 113.23 - 120.17: 1892 120.17 - 127.11: 2501 127.11 - 134.05: 67 Bond angle restraints: 7817 Sorted by residual: angle pdb=" CA GLU A 257 " pdb=" CB GLU A 257 " pdb=" CG GLU A 257 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA LEU A 165 " pdb=" CB LEU A 165 " pdb=" CG LEU A 165 " ideal model delta sigma weight residual 116.30 126.33 -10.03 3.50e+00 8.16e-02 8.21e+00 angle pdb=" CB GLU A 257 " pdb=" CG GLU A 257 " pdb=" CD GLU A 257 " ideal model delta sigma weight residual 112.60 116.99 -4.39 1.70e+00 3.46e-01 6.68e+00 angle pdb=" CA TYR L 31 " pdb=" CB TYR L 31 " pdb=" CG TYR L 31 " ideal model delta sigma weight residual 113.90 118.30 -4.40 1.80e+00 3.09e-01 5.97e+00 angle pdb=" CA GLY H 115 " pdb=" C GLY H 115 " pdb=" O GLY H 115 " ideal model delta sigma weight residual 122.22 120.63 1.59 6.50e-01 2.37e+00 5.95e+00 ... (remaining 7812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 2913 16.35 - 32.69: 367 32.69 - 49.04: 124 49.04 - 65.38: 28 65.38 - 81.73: 4 Dihedral angle restraints: 3436 sinusoidal: 1310 harmonic: 2126 Sorted by residual: dihedral pdb=" CB CYS H 149 " pdb=" SG CYS H 149 " pdb=" SG CYS H 204 " pdb=" CB CYS H 204 " ideal model delta sinusoidal sigma weight residual 93.00 160.94 -67.94 1 1.00e+01 1.00e-02 5.99e+01 dihedral pdb=" CA ASN L 30 " pdb=" C ASN L 30 " pdb=" N TYR L 31 " pdb=" CA TYR L 31 " ideal model delta harmonic sigma weight residual 180.00 158.47 21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA GLY A 132 " pdb=" C GLY A 132 " pdb=" N MET A 133 " pdb=" CA MET A 133 " ideal model delta harmonic sigma weight residual -180.00 -162.30 -17.70 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 3433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 533 0.027 - 0.054: 241 0.054 - 0.080: 70 0.080 - 0.107: 44 0.107 - 0.134: 20 Chirality restraints: 908 Sorted by residual: chirality pdb=" CA VAL H 206 " pdb=" N VAL H 206 " pdb=" C VAL H 206 " pdb=" CB VAL H 206 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA VAL H 161 " pdb=" N VAL H 161 " pdb=" C VAL H 161 " pdb=" CB VAL H 161 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA PRO A 220 " pdb=" N PRO A 220 " pdb=" C PRO A 220 " pdb=" CB PRO A 220 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 905 not shown) Planarity restraints: 965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS H 208 " 0.063 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO H 209 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO H 209 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO H 209 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 219 " -0.046 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO A 220 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 180 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO A 181 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.035 5.00e-02 4.00e+02 ... (remaining 962 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1142 2.78 - 3.31: 4982 3.31 - 3.84: 9209 3.84 - 4.37: 10533 4.37 - 4.90: 18948 Nonbonded interactions: 44814 Sorted by model distance: nonbonded pdb=" OG SER L 62 " pdb=" OG1 THR L 73 " model vdw 2.250 2.440 nonbonded pdb=" OE1 GLN A 68 " pdb=" OG SER A 126 " model vdw 2.260 2.440 nonbonded pdb=" O SER H 85 " pdb=" OG SER H 85 " model vdw 2.266 2.440 nonbonded pdb=" OG SER L 120 " pdb=" O PRO H 132 " model vdw 2.271 2.440 nonbonded pdb=" NH1 ARG L 107 " pdb=" O ASP L 169 " model vdw 2.271 2.520 ... (remaining 44809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.720 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: 0.010 Extract box with map and model: 3.760 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 20.010 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5749 Z= 0.180 Angle : 0.596 10.026 7817 Z= 0.317 Chirality : 0.040 0.134 908 Planarity : 0.006 0.096 965 Dihedral : 16.431 81.730 2062 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.55 % Allowed : 27.79 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.59 (0.32), residues: 728 helix: 1.93 (0.34), residues: 258 sheet: 0.27 (0.38), residues: 198 loop : -1.02 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 162 HIS 0.002 0.001 HIS L 33 PHE 0.018 0.001 PHE H 155 TYR 0.012 0.001 TYR H 184 ARG 0.002 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 72 time to evaluate : 0.689 Fit side-chains REVERT: L 4 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7425 (mtp) REVERT: H 107 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.6248 (p90) outliers start: 29 outliers final: 25 residues processed: 98 average time/residue: 0.1441 time to fit residues: 20.0671 Evaluate side-chains 99 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 72 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 117 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.0000 chunk 42 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.0544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5749 Z= 0.183 Angle : 0.532 7.983 7817 Z= 0.272 Chirality : 0.041 0.148 908 Planarity : 0.006 0.066 965 Dihedral : 8.515 69.496 822 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.71 % Allowed : 27.63 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.82 (0.33), residues: 728 helix: 2.03 (0.33), residues: 266 sheet: 0.25 (0.36), residues: 221 loop : -0.82 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 90 HIS 0.002 0.001 HIS L 88 PHE 0.011 0.001 PHE H 107 TYR 0.012 0.001 TYR H 154 ARG 0.002 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 78 time to evaluate : 0.701 Fit side-chains REVERT: A 257 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7522 (tm-30) REVERT: L 4 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7725 (mtp) REVERT: L 174 MET cc_start: 0.6754 (tpt) cc_final: 0.6287 (tpt) outliers start: 30 outliers final: 19 residues processed: 104 average time/residue: 0.1384 time to fit residues: 20.1894 Evaluate side-chains 93 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 205 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 44 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5749 Z= 0.229 Angle : 0.538 7.164 7817 Z= 0.275 Chirality : 0.041 0.147 908 Planarity : 0.005 0.057 965 Dihedral : 7.326 69.746 799 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.87 % Allowed : 27.00 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.84 (0.33), residues: 728 helix: 2.02 (0.32), residues: 266 sheet: 0.32 (0.36), residues: 221 loop : -0.83 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 90 HIS 0.003 0.001 HIS L 88 PHE 0.012 0.001 PHE H 107 TYR 0.012 0.001 TYR H 154 ARG 0.001 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 75 time to evaluate : 0.641 Fit side-chains REVERT: A 257 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7523 (tm-30) REVERT: L 4 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8281 (mtp) outliers start: 31 outliers final: 23 residues processed: 102 average time/residue: 0.1347 time to fit residues: 19.5534 Evaluate side-chains 97 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 73 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 205 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 30.0000 chunk 34 optimal weight: 0.0050 chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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: 0.7238 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5749 Z= 0.213 Angle : 0.529 6.867 7817 Z= 0.269 Chirality : 0.041 0.149 908 Planarity : 0.005 0.052 965 Dihedral : 6.848 69.866 794 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.71 % Allowed : 27.47 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.87 (0.32), residues: 728 helix: 2.07 (0.32), residues: 266 sheet: 0.33 (0.36), residues: 221 loop : -0.84 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 162 HIS 0.002 0.001 HIS L 33 PHE 0.011 0.001 PHE H 107 TYR 0.012 0.001 TYR H 154 ARG 0.001 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 74 time to evaluate : 0.689 Fit side-chains REVERT: A 143 ARG cc_start: 0.5609 (OUTLIER) cc_final: 0.4938 (ptt90) REVERT: A 196 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7367 (tm) REVERT: A 257 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7521 (tm-30) REVERT: L 169 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7336 (p0) outliers start: 30 outliers final: 21 residues processed: 99 average time/residue: 0.1444 time to fit residues: 19.8210 Evaluate side-chains 97 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 73 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 205 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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: 0.7265 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5749 Z= 0.281 Angle : 0.563 7.795 7817 Z= 0.286 Chirality : 0.042 0.153 908 Planarity : 0.005 0.049 965 Dihedral : 6.022 69.813 787 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.49 % Allowed : 27.00 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.76 (0.32), residues: 728 helix: 1.97 (0.32), residues: 266 sheet: 0.25 (0.36), residues: 221 loop : -0.86 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 162 HIS 0.002 0.001 HIS A 54 PHE 0.012 0.001 PHE H 107 TYR 0.013 0.001 TYR H 95 ARG 0.001 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 78 time to evaluate : 0.635 Fit side-chains REVERT: A 143 ARG cc_start: 0.5665 (OUTLIER) cc_final: 0.4977 (ptt90) REVERT: A 184 MET cc_start: 0.2175 (tmt) cc_final: 0.1641 (ttt) REVERT: A 196 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7306 (tm) REVERT: A 257 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7520 (tm-30) REVERT: L 4 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8150 (mtp) REVERT: L 169 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7304 (p0) outliers start: 35 outliers final: 23 residues processed: 109 average time/residue: 0.1337 time to fit residues: 20.4321 Evaluate side-chains 100 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 73 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 205 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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: 0.7258 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5749 Z= 0.246 Angle : 0.559 8.460 7817 Z= 0.282 Chirality : 0.041 0.153 908 Planarity : 0.005 0.049 965 Dihedral : 5.978 69.803 787 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.18 % Allowed : 27.47 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.72 (0.32), residues: 728 helix: 1.93 (0.32), residues: 266 sheet: 0.25 (0.36), residues: 223 loop : -0.92 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 162 HIS 0.002 0.001 HIS L 33 PHE 0.012 0.001 PHE H 107 TYR 0.012 0.001 TYR H 154 ARG 0.001 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 73 time to evaluate : 0.651 Fit side-chains REVERT: A 143 ARG cc_start: 0.5652 (OUTLIER) cc_final: 0.4974 (ptt90) REVERT: A 184 MET cc_start: 0.2239 (tmt) cc_final: 0.1734 (ttt) REVERT: A 257 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7517 (tm-30) REVERT: L 4 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8144 (mtp) REVERT: L 169 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7332 (p0) REVERT: L 174 MET cc_start: 0.7017 (tpt) cc_final: 0.6226 (tpt) REVERT: H 5 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6743 (tt0) outliers start: 33 outliers final: 23 residues processed: 103 average time/residue: 0.1378 time to fit residues: 19.8004 Evaluate side-chains 100 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 73 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 205 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 41 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7234 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5749 Z= 0.193 Angle : 0.548 9.580 7817 Z= 0.273 Chirality : 0.040 0.151 908 Planarity : 0.005 0.049 965 Dihedral : 5.829 69.830 787 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.71 % Allowed : 27.94 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.78 (0.33), residues: 728 helix: 2.00 (0.32), residues: 266 sheet: 0.27 (0.36), residues: 223 loop : -0.89 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 162 HIS 0.002 0.001 HIS L 33 PHE 0.010 0.001 PHE H 107 TYR 0.012 0.001 TYR H 154 ARG 0.001 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 74 time to evaluate : 0.640 Fit side-chains REVERT: A 116 MET cc_start: 0.8107 (mmm) cc_final: 0.7867 (mmm) REVERT: A 143 ARG cc_start: 0.5615 (OUTLIER) cc_final: 0.4995 (ptt90) REVERT: A 184 MET cc_start: 0.2238 (tmt) cc_final: 0.1774 (ttt) REVERT: A 257 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7479 (tm-30) REVERT: L 4 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8187 (mtp) REVERT: L 169 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7359 (p0) REVERT: L 174 MET cc_start: 0.7005 (tpt) cc_final: 0.6256 (tpt) REVERT: H 5 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6761 (tt0) outliers start: 30 outliers final: 21 residues processed: 102 average time/residue: 0.1430 time to fit residues: 20.3685 Evaluate side-chains 98 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 73 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 206 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 0.0870 chunk 63 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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: 0.7284 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5749 Z= 0.346 Angle : 0.612 10.481 7817 Z= 0.308 Chirality : 0.043 0.155 908 Planarity : 0.005 0.049 965 Dihedral : 6.044 69.690 787 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 5.02 % Allowed : 27.79 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.57 (0.32), residues: 728 helix: 1.75 (0.32), residues: 266 sheet: 0.18 (0.36), residues: 223 loop : -0.95 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 90 HIS 0.002 0.001 HIS L 88 PHE 0.014 0.001 PHE H 107 TYR 0.014 0.002 TYR H 95 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 73 time to evaluate : 0.654 Fit side-chains REVERT: A 143 ARG cc_start: 0.5721 (OUTLIER) cc_final: 0.5023 (ptt90) REVERT: A 184 MET cc_start: 0.2262 (tmt) cc_final: 0.1814 (ttt) REVERT: A 257 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7518 (tm-30) REVERT: L 4 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8144 (mtp) REVERT: L 169 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7297 (p0) REVERT: L 174 MET cc_start: 0.7006 (tpt) cc_final: 0.6332 (tpt) REVERT: H 5 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6724 (tt0) outliers start: 32 outliers final: 25 residues processed: 102 average time/residue: 0.1456 time to fit residues: 20.4898 Evaluate side-chains 102 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 73 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 206 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 20.0000 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 64 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7239 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5749 Z= 0.191 Angle : 0.566 10.768 7817 Z= 0.280 Chirality : 0.041 0.150 908 Planarity : 0.005 0.050 965 Dihedral : 5.864 70.168 787 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.92 % Allowed : 29.04 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.67 (0.32), residues: 728 helix: 1.90 (0.32), residues: 266 sheet: 0.21 (0.36), residues: 223 loop : -0.94 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 162 HIS 0.002 0.001 HIS L 33 PHE 0.010 0.001 PHE H 107 TYR 0.012 0.001 TYR H 154 ARG 0.001 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 73 time to evaluate : 0.662 Fit side-chains REVERT: A 143 ARG cc_start: 0.5653 (OUTLIER) cc_final: 0.5011 (ptt90) REVERT: A 184 MET cc_start: 0.2292 (tmt) cc_final: 0.1810 (ttt) REVERT: A 256 MET cc_start: 0.7154 (mmm) cc_final: 0.6838 (mmm) REVERT: A 257 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7502 (tm-30) REVERT: L 4 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8154 (mtp) REVERT: L 169 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7350 (p0) REVERT: L 174 MET cc_start: 0.7020 (tpt) cc_final: 0.6288 (tpt) REVERT: H 5 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6742 (tt0) outliers start: 25 outliers final: 20 residues processed: 97 average time/residue: 0.1423 time to fit residues: 19.2285 Evaluate side-chains 96 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 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 : 0.006 0.042 5749 Z= 0.380 Angle : 0.642 11.110 7817 Z= 0.322 Chirality : 0.043 0.155 908 Planarity : 0.005 0.049 965 Dihedral : 5.999 69.982 786 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.08 % Allowed : 29.36 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.44 (0.32), residues: 728 helix: 1.69 (0.32), residues: 266 sheet: 0.08 (0.36), residues: 223 loop : -1.04 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 90 HIS 0.003 0.001 HIS L 33 PHE 0.014 0.002 PHE H 107 TYR 0.014 0.002 TYR H 95 ARG 0.002 0.000 ARG A 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 76 time to evaluate : 0.690 Fit side-chains REVERT: A 143 ARG cc_start: 0.5679 (OUTLIER) cc_final: 0.4985 (ptt90) REVERT: A 184 MET cc_start: 0.2405 (tmt) cc_final: 0.1915 (ttt) REVERT: A 256 MET cc_start: 0.7244 (mmm) cc_final: 0.6893 (mmm) REVERT: A 257 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7528 (tm-30) REVERT: L 4 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8122 (mtp) REVERT: L 174 MET cc_start: 0.7009 (tpt) cc_final: 0.6346 (tpt) REVERT: H 5 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.6730 (tt0) outliers start: 26 outliers final: 21 residues processed: 100 average time/residue: 0.1477 time to fit residues: 20.4621 Evaluate side-chains 98 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 74 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.166079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.124631 restraints weight = 6031.429| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.57 r_work: 0.2856 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5749 Z= 0.238 Angle : 0.598 11.221 7817 Z= 0.297 Chirality : 0.042 0.153 908 Planarity : 0.005 0.050 965 Dihedral : 5.898 69.971 786 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.77 % Allowed : 30.46 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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 (0.32), residues: 728 helix: 1.77 (0.32), residues: 266 sheet: 0.12 (0.36), residues: 223 loop : -1.03 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 90 HIS 0.002 0.001 HIS L 33 PHE 0.012 0.001 PHE H 107 TYR 0.012 0.001 TYR H 154 ARG 0.001 0.000 ARG A 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1452.59 seconds wall clock time: 27 minutes 6.24 seconds (1626.24 seconds total)