Starting phenix.real_space_refine on Tue Feb 13 07:22:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dls_27514/02_2024/8dls_27514.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dls_27514/02_2024/8dls_27514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dls_27514/02_2024/8dls_27514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dls_27514/02_2024/8dls_27514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dls_27514/02_2024/8dls_27514.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dls_27514/02_2024/8dls_27514.pdb" } resolution = 2.66 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= 0.016 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 18 5.16 5 C 2566 2.51 5 N 648 2.21 5 O 785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 129": "OD1" <-> "OD2" Residue "H TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 4017 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2081 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 12, 'TRANS': 242} Chain breaks: 3 Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 976 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.73, per 1000 atoms: 0.68 Number of scatterers: 4017 At special positions: 0 Unit cell: (95, 61, 101, 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 18 16.00 O 785 8.00 N 648 7.00 C 2566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 113 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 149 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 824.9 milliseconds 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 10 sheets defined 2.6% alpha, 45.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.910A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 108 removed outlier: 3.963A pdb=" N VAL L 108 " --> pdb=" O ALA L 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 8.072A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.764A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.606A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.627A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.164A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 141 " --> pdb=" O TYR H 113 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET H 53 " --> pdb=" O GLY H 69 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP H 55 " --> pdb=" O MET H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.164A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 141 " --> pdb=" O TYR H 113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 121 through 123 Processing sheet with id=AA9, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 32 removed outlier: 3.758A pdb=" N ASP L 130 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN L 62 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU L 71 " --> pdb=" O GLN L 62 " (cutoff:3.500A) 144 hydrogen bonds defined for protein. 357 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: 1.13 Time building geometry restraints manager: 1.64 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: 1235 1.34 - 1.46: 1022 1.46 - 1.58: 1834 1.58 - 1.70: 0 1.70 - 1.81: 27 Bond restraints: 4118 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.24e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" C ARG A 102 " pdb=" N GLY A 103 " ideal model delta sigma weight residual 1.327 1.307 0.020 1.11e-02 8.12e+03 3.25e+00 ... (remaining 4113 not shown) Histogram of bond angle deviations from ideal: 98.65 - 105.71: 88 105.71 - 112.77: 2131 112.77 - 119.82: 1326 119.82 - 126.88: 1996 126.88 - 133.94: 56 Bond angle restraints: 5597 Sorted by residual: angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 121.54 132.21 -10.67 1.91e+00 2.74e-01 3.12e+01 angle pdb=" CA LEU H 127 " pdb=" CB LEU H 127 " pdb=" CG LEU H 127 " ideal model delta sigma weight residual 116.30 128.67 -12.37 3.50e+00 8.16e-02 1.25e+01 angle pdb=" C GLN H 139 " pdb=" N GLY H 140 " pdb=" CA GLY H 140 " ideal model delta sigma weight residual 122.73 119.73 3.00 9.30e-01 1.16e+00 1.04e+01 angle pdb=" CA THR L 56 " pdb=" CB THR L 56 " pdb=" CG2 THR L 56 " ideal model delta sigma weight residual 110.50 115.81 -5.31 1.70e+00 3.46e-01 9.77e+00 angle pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " pdb=" CG ASP A 198 " ideal model delta sigma weight residual 112.60 115.70 -3.10 1.00e+00 1.00e+00 9.64e+00 ... (remaining 5592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 2319 17.40 - 34.79: 149 34.79 - 52.18: 26 52.18 - 69.57: 5 69.57 - 86.97: 5 Dihedral angle restraints: 2504 sinusoidal: 1066 harmonic: 1438 Sorted by residual: dihedral pdb=" CA ASN A 149 " pdb=" C ASN A 149 " pdb=" N LYS A 150 " pdb=" CA LYS A 150 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA LYS H 31 " pdb=" C LYS H 31 " pdb=" N LYS H 32 " pdb=" CA LYS H 32 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ILE A 128 " pdb=" C ILE A 128 " pdb=" N LYS A 129 " pdb=" CA LYS A 129 " ideal model delta harmonic sigma weight residual 180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 2501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 572 0.097 - 0.193: 57 0.193 - 0.290: 3 0.290 - 0.386: 0 0.386 - 0.483: 3 Chirality restraints: 635 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 149 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CB THR L 56 " pdb=" CA THR L 56 " pdb=" OG1 THR L 56 " pdb=" CG2 THR L 56 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 632 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 149 " 0.005 2.00e-02 2.50e+03 2.66e-02 8.87e+00 pdb=" CG ASN A 149 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 149 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN A 149 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 198 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" CG ASP A 198 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASP A 198 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 198 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 83 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO L 84 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 84 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 84 " 0.035 5.00e-02 4.00e+02 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1088 2.81 - 3.33: 3098 3.33 - 3.86: 6567 3.86 - 4.38: 7546 4.38 - 4.90: 13461 Nonbonded interactions: 31760 Sorted by model distance: nonbonded pdb=" OD1 ASP H 109 " pdb=" OH TYR H 113 " model vdw 2.288 2.440 nonbonded pdb=" OG SER L 90 " pdb=" OG1 THR L 97 " model vdw 2.323 2.440 nonbonded pdb=" OG1 THR H 124 " pdb=" O ASP H 126 " model vdw 2.327 2.440 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.362 2.440 nonbonded pdb=" O SER H 147 " pdb=" OG SER H 147 " model vdw 2.374 2.440 ... (remaining 31755 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: 2.740 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: 12.940 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.760 Find NCS groups from input model: 0.110 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:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.006 0.057 4118 Z= 0.395 Angle : 0.916 12.370 5597 Z= 0.486 Chirality : 0.063 0.483 635 Planarity : 0.007 0.069 705 Dihedral : 12.285 86.966 1572 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.59 (0.37), residues: 483 helix: None (None), residues: 0 sheet: 0.15 (0.36), residues: 218 loop : -0.84 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 66 HIS 0.005 0.002 HIS L 51 PHE 0.028 0.003 PHE A 238 TYR 0.020 0.002 TYR A 160 ARG 0.014 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.518 Fit side-chains REVERT: A 15 CYS cc_start: 0.7351 (m) cc_final: 0.7117 (m) REVERT: A 153 MET cc_start: 0.8371 (mmt) cc_final: 0.8037 (mmm) REVERT: H 99 TYR cc_start: 0.7958 (m-80) cc_final: 0.7599 (m-80) REVERT: L 63 GLN cc_start: 0.8931 (tt0) cc_final: 0.8728 (tt0) REVERT: L 75 LYS cc_start: 0.8501 (mttt) cc_final: 0.8168 (mtpt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 1.0351 time to fit residues: 105.2690 Evaluate side-chains 83 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 207 HIS L 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4118 Z= 0.248 Angle : 0.602 10.480 5597 Z= 0.307 Chirality : 0.049 0.380 635 Planarity : 0.004 0.047 705 Dihedral : 6.370 48.931 684 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.07 % Allowed : 9.43 % Favored : 88.51 % 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 (0.38), residues: 483 helix: None (None), residues: 0 sheet: 0.27 (0.35), residues: 225 loop : -0.40 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 66 HIS 0.002 0.001 HIS A 49 PHE 0.014 0.001 PHE A 175 TYR 0.010 0.001 TYR A 269 ARG 0.003 0.000 ARG L 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.468 Fit side-chains REVERT: A 214 ARG cc_start: 0.7209 (tpp-160) cc_final: 0.6948 (tpp-160) REVERT: H 48 LEU cc_start: 0.8666 (tp) cc_final: 0.8300 (tt) REVERT: H 99 TYR cc_start: 0.7914 (m-80) cc_final: 0.7622 (m-80) REVERT: H 130 TYR cc_start: 0.8107 (m-80) cc_final: 0.7874 (m-80) REVERT: L 63 GLN cc_start: 0.8929 (tt0) cc_final: 0.8698 (tt0) REVERT: L 75 LYS cc_start: 0.8376 (mttt) cc_final: 0.8067 (mmmt) outliers start: 9 outliers final: 9 residues processed: 87 average time/residue: 1.0065 time to fit residues: 91.3025 Evaluate side-chains 86 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.0030 chunk 32 optimal weight: 2.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4118 Z= 0.202 Angle : 0.571 9.861 5597 Z= 0.289 Chirality : 0.047 0.343 635 Planarity : 0.004 0.042 705 Dihedral : 6.011 49.389 684 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.30 % Allowed : 12.64 % Favored : 85.06 % 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: 0.06 (0.39), residues: 483 helix: None (None), residues: 0 sheet: 0.42 (0.36), residues: 222 loop : -0.22 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.002 0.001 HIS L 51 PHE 0.012 0.001 PHE A 175 TYR 0.012 0.001 TYR H 132 ARG 0.004 0.000 ARG L 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.452 Fit side-chains REVERT: A 218 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: H 48 LEU cc_start: 0.8713 (tp) cc_final: 0.8295 (tt) REVERT: H 130 TYR cc_start: 0.8156 (m-80) cc_final: 0.7765 (m-80) REVERT: L 63 GLN cc_start: 0.8958 (tt0) cc_final: 0.8696 (tt0) outliers start: 10 outliers final: 7 residues processed: 86 average time/residue: 0.9652 time to fit residues: 86.4546 Evaluate side-chains 87 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 chunk 43 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 0.0170 chunk 0 optimal weight: 4.9990 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4118 Z= 0.177 Angle : 0.558 10.680 5597 Z= 0.279 Chirality : 0.046 0.332 635 Planarity : 0.004 0.040 705 Dihedral : 5.766 49.863 684 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.99 % Allowed : 12.87 % Favored : 84.14 % 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: 0.23 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.49 (0.36), residues: 221 loop : -0.05 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 HIS 0.001 0.001 HIS L 51 PHE 0.016 0.001 PHE L 96 TYR 0.008 0.001 TYR A 269 ARG 0.003 0.000 ARG L 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 211 ASN cc_start: 0.8313 (t0) cc_final: 0.8112 (t0) REVERT: A 218 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: H 48 LEU cc_start: 0.8710 (tp) cc_final: 0.8281 (tt) REVERT: H 65 GLU cc_start: 0.7977 (pt0) cc_final: 0.7676 (pt0) REVERT: H 130 TYR cc_start: 0.8189 (m-80) cc_final: 0.7804 (m-80) REVERT: H 132 TYR cc_start: 0.8841 (m-80) cc_final: 0.8609 (m-80) REVERT: L 63 GLN cc_start: 0.8918 (tt0) cc_final: 0.8664 (tt0) outliers start: 13 outliers final: 9 residues processed: 86 average time/residue: 0.9421 time to fit residues: 84.3897 Evaluate side-chains 86 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8049 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4118 Z= 0.224 Angle : 0.581 11.582 5597 Z= 0.288 Chirality : 0.046 0.329 635 Planarity : 0.004 0.040 705 Dihedral : 5.706 49.110 684 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.22 % Allowed : 13.56 % Favored : 83.22 % 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: 0.36 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.65 (0.37), residues: 209 loop : -0.01 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 66 HIS 0.002 0.001 HIS H 54 PHE 0.014 0.001 PHE L 96 TYR 0.011 0.001 TYR H 79 ARG 0.003 0.000 ARG L 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 218 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: H 48 LEU cc_start: 0.8709 (tp) cc_final: 0.8282 (tt) REVERT: H 130 TYR cc_start: 0.8262 (m-80) cc_final: 0.7865 (m-80) REVERT: L 55 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7408 (p0) REVERT: L 63 GLN cc_start: 0.8998 (tt0) cc_final: 0.8676 (tt0) outliers start: 14 outliers final: 10 residues processed: 82 average time/residue: 1.0923 time to fit residues: 92.9826 Evaluate side-chains 88 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.0040 chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 33 optimal weight: 0.2980 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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: 0.8037 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4118 Z= 0.175 Angle : 0.570 12.100 5597 Z= 0.282 Chirality : 0.046 0.324 635 Planarity : 0.004 0.040 705 Dihedral : 5.596 49.805 684 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.22 % Allowed : 14.25 % Favored : 82.53 % 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: 0.39 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.65 (0.37), residues: 209 loop : 0.02 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 137 HIS 0.002 0.001 HIS H 54 PHE 0.010 0.001 PHE A 175 TYR 0.008 0.001 TYR A 269 ARG 0.003 0.000 ARG L 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 211 ASN cc_start: 0.8197 (t0) cc_final: 0.7973 (t0) REVERT: A 215 ASP cc_start: 0.7671 (m-30) cc_final: 0.7366 (m-30) REVERT: A 218 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7828 (mp10) REVERT: H 48 LEU cc_start: 0.8694 (tp) cc_final: 0.8255 (tt) REVERT: H 130 TYR cc_start: 0.8255 (m-80) cc_final: 0.7882 (m-80) REVERT: L 55 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7466 (p0) REVERT: L 63 GLN cc_start: 0.8991 (tt0) cc_final: 0.8729 (tt0) outliers start: 14 outliers final: 12 residues processed: 83 average time/residue: 1.0314 time to fit residues: 89.0240 Evaluate side-chains 90 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 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: 0.8060 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4118 Z= 0.264 Angle : 0.591 12.673 5597 Z= 0.292 Chirality : 0.047 0.327 635 Planarity : 0.004 0.041 705 Dihedral : 5.627 47.953 684 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.14 % Allowed : 14.94 % Favored : 80.92 % 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: 0.37 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.59 (0.38), residues: 206 loop : 0.07 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 137 HIS 0.003 0.001 HIS H 54 PHE 0.016 0.001 PHE A 175 TYR 0.011 0.001 TYR H 79 ARG 0.004 0.000 ARG L 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 218 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7881 (mp10) REVERT: H 48 LEU cc_start: 0.8704 (tp) cc_final: 0.8280 (tt) REVERT: H 130 TYR cc_start: 0.8320 (m-80) cc_final: 0.8006 (m-80) REVERT: L 55 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7594 (p0) REVERT: L 63 GLN cc_start: 0.8914 (tt0) cc_final: 0.8617 (tt0) outliers start: 18 outliers final: 11 residues processed: 80 average time/residue: 1.0366 time to fit residues: 86.2433 Evaluate side-chains 87 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS L 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4118 Z= 0.297 Angle : 0.615 13.053 5597 Z= 0.306 Chirality : 0.047 0.327 635 Planarity : 0.004 0.042 705 Dihedral : 5.755 46.839 684 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.37 % Allowed : 16.09 % Favored : 79.54 % 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: 0.36 (0.39), residues: 483 helix: None (None), residues: 0 sheet: 0.57 (0.38), residues: 193 loop : 0.10 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 66 HIS 0.003 0.001 HIS H 54 PHE 0.018 0.001 PHE A 175 TYR 0.013 0.001 TYR H 79 ARG 0.004 0.000 ARG L 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 151 SER cc_start: 0.8240 (t) cc_final: 0.7511 (p) REVERT: A 154 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8826 (mt-10) REVERT: A 218 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: H 48 LEU cc_start: 0.8714 (tp) cc_final: 0.8276 (tt) REVERT: L 55 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7571 (p0) REVERT: L 63 GLN cc_start: 0.8921 (tt0) cc_final: 0.8626 (tt0) outliers start: 19 outliers final: 11 residues processed: 84 average time/residue: 0.9975 time to fit residues: 86.8998 Evaluate side-chains 92 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.0970 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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: 0.8059 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4118 Z= 0.243 Angle : 0.610 13.733 5597 Z= 0.304 Chirality : 0.047 0.319 635 Planarity : 0.004 0.042 705 Dihedral : 5.702 47.348 684 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.91 % Allowed : 16.09 % Favored : 80.00 % 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: 0.33 (0.39), residues: 483 helix: None (None), residues: 0 sheet: 0.53 (0.38), residues: 199 loop : 0.08 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.002 0.001 HIS A 245 PHE 0.015 0.001 PHE A 175 TYR 0.017 0.001 TYR H 99 ARG 0.004 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 151 SER cc_start: 0.8236 (t) cc_final: 0.7497 (p) REVERT: A 154 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8806 (mt-10) REVERT: A 218 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7881 (mp10) REVERT: H 31 LYS cc_start: 0.7657 (pmmt) cc_final: 0.7320 (pmtt) REVERT: H 48 LEU cc_start: 0.8701 (tp) cc_final: 0.8260 (tt) REVERT: H 130 TYR cc_start: 0.8282 (m-80) cc_final: 0.8003 (m-80) REVERT: L 55 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.7602 (p0) REVERT: L 63 GLN cc_start: 0.8911 (tt0) cc_final: 0.8610 (tt0) outliers start: 17 outliers final: 10 residues processed: 83 average time/residue: 1.0047 time to fit residues: 86.7134 Evaluate side-chains 89 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.0040 chunk 23 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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: 0.8058 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4118 Z= 0.244 Angle : 0.619 14.011 5597 Z= 0.307 Chirality : 0.047 0.319 635 Planarity : 0.004 0.042 705 Dihedral : 5.665 47.351 684 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.68 % Allowed : 17.01 % Favored : 79.31 % 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: 0.39 (0.39), residues: 483 helix: None (None), residues: 0 sheet: 0.57 (0.38), residues: 199 loop : 0.12 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 137 HIS 0.003 0.001 HIS H 54 PHE 0.015 0.001 PHE A 175 TYR 0.010 0.001 TYR H 132 ARG 0.007 0.001 ARG A 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 151 SER cc_start: 0.8241 (t) cc_final: 0.7501 (p) REVERT: A 154 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8798 (mt-10) REVERT: A 218 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7872 (mp10) REVERT: H 48 LEU cc_start: 0.8695 (tp) cc_final: 0.8277 (tt) REVERT: H 130 TYR cc_start: 0.8246 (m-80) cc_final: 0.7989 (m-80) REVERT: L 55 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.7637 (p0) REVERT: L 63 GLN cc_start: 0.8909 (tt0) cc_final: 0.8606 (tt0) outliers start: 16 outliers final: 10 residues processed: 83 average time/residue: 1.0106 time to fit residues: 87.3455 Evaluate side-chains 89 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.119190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.076704 restraints weight = 6371.421| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.78 r_work: 0.2887 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 4118 Z= 0.375 Angle : 0.656 14.265 5597 Z= 0.326 Chirality : 0.049 0.322 635 Planarity : 0.004 0.045 705 Dihedral : 5.931 44.073 684 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.22 % Allowed : 16.55 % Favored : 80.23 % 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: 0.33 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.50 (0.38), residues: 201 loop : 0.10 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 55 HIS 0.004 0.001 HIS H 54 PHE 0.024 0.002 PHE A 175 TYR 0.015 0.002 TYR H 99 ARG 0.006 0.001 ARG L 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2312.07 seconds wall clock time: 41 minutes 27.73 seconds (2487.73 seconds total)