Starting phenix.real_space_refine on Fri Jul 19 01:35:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/07_2024/8t05_40935_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/07_2024/8t05_40935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/07_2024/8t05_40935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/07_2024/8t05_40935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/07_2024/8t05_40935_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/07_2024/8t05_40935_neut.cif" } resolution = 3.22 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= 0.004 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 22 5.16 5 C 3387 2.51 5 N 798 2.21 5 O 893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 5104 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "B" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "C" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 3.89, per 1000 atoms: 0.76 Number of scatterers: 5104 At special positions: 0 Unit cell: (81.34, 88.81, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 22 16.00 P 2 15.00 O 893 8.00 N 798 7.00 C 3387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 60 " distance=2.04 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 60 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 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: 2.32 Conformation dependent library (CDL) restraints added in 992.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 182 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 186 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 186 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 182 " 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1158 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 55.6% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.844A pdb=" N VAL A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 18 through 28 removed outlier: 3.546A pdb=" N GLY A 22 " --> pdb=" O PHE A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 51 removed outlier: 4.083A pdb=" N LEU A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.692A pdb=" N MET A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 86 removed outlier: 3.738A pdb=" N THR A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 112 removed outlier: 3.555A pdb=" N GLU A 112 " --> pdb=" O ARG A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 142 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 177 through 198 removed outlier: 3.787A pdb=" N SER A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 14 Proline residue: B 11 - end of helix Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 18 through 28 removed outlier: 3.721A pdb=" N GLY B 22 " --> pdb=" O PHE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 52 Processing helix chain 'B' and resid 63 through 86 removed outlier: 3.628A pdb=" N PHE B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 112 Processing helix chain 'B' and resid 119 through 141 Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 154 through 171 Processing helix chain 'B' and resid 177 through 197 removed outlier: 3.965A pdb=" N SER B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.885A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 11 removed outlier: 5.688A pdb=" N GLU C 10 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA C 92 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.072A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.533A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) 298 hydrogen bonds defined for protein. 864 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: 1.29 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 746 1.31 - 1.44: 1499 1.44 - 1.56: 2946 1.56 - 1.69: 14 1.69 - 1.82: 32 Bond restraints: 5237 Sorted by residual: bond pdb=" C GLY C 8 " pdb=" N ALA C 9 " ideal model delta sigma weight residual 1.331 1.409 -0.077 1.30e-02 5.92e+03 3.53e+01 bond pdb=" C25 LBN A 303 " pdb=" O5 LBN A 303 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C25 LBN B 303 " pdb=" O5 LBN B 303 " ideal model delta sigma weight residual 1.326 1.429 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C34 LBN A 303 " pdb=" O7 LBN A 303 " ideal model delta sigma weight residual 1.331 1.427 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C34 LBN B 303 " pdb=" O7 LBN B 303 " ideal model delta sigma weight residual 1.331 1.424 -0.093 2.00e-02 2.50e+03 2.16e+01 ... (remaining 5232 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.22: 126 106.22 - 113.28: 2774 113.28 - 120.34: 2328 120.34 - 127.40: 1834 127.40 - 134.45: 43 Bond angle restraints: 7105 Sorted by residual: angle pdb=" N PHE C 109 " pdb=" CA PHE C 109 " pdb=" C PHE C 109 " ideal model delta sigma weight residual 111.24 118.85 -7.61 1.38e+00 5.25e-01 3.04e+01 angle pdb=" C GLY A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta sigma weight residual 120.03 125.59 -5.56 1.12e+00 7.97e-01 2.47e+01 angle pdb=" N THR D 94 " pdb=" CA THR D 94 " pdb=" C THR D 94 " ideal model delta sigma weight residual 108.82 117.00 -8.18 1.65e+00 3.67e-01 2.46e+01 angle pdb=" O1 LBN B 303 " pdb=" P1 LBN B 303 " pdb=" O2 LBN B 303 " ideal model delta sigma weight residual 93.45 108.05 -14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" O1 LBN A 303 " pdb=" P1 LBN A 303 " pdb=" O2 LBN A 303 " ideal model delta sigma weight residual 93.45 107.88 -14.43 3.00e+00 1.11e-01 2.31e+01 ... (remaining 7100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.48: 3038 30.48 - 60.96: 92 60.96 - 91.44: 11 91.44 - 121.92: 7 121.92 - 152.40: 4 Dihedral angle restraints: 3152 sinusoidal: 1337 harmonic: 1815 Sorted by residual: dihedral pdb=" CA THR D 94 " pdb=" C THR D 94 " pdb=" N PRO D 95 " pdb=" CA PRO D 95 " ideal model delta harmonic sigma weight residual 180.00 70.79 109.21 0 5.00e+00 4.00e-02 4.77e+02 dihedral pdb=" CA ALA D 50 " pdb=" C ALA D 50 " pdb=" N ALA D 51 " pdb=" CA ALA D 51 " ideal model delta harmonic sigma weight residual -180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA SER B 56 " pdb=" C SER B 56 " pdb=" N LEU B 57 " pdb=" CA LEU B 57 " ideal model delta harmonic sigma weight residual -180.00 -155.12 -24.88 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 3149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.985: 803 0.985 - 1.969: 0 1.969 - 2.954: 0 2.954 - 3.938: 0 3.938 - 4.923: 2 Chirality restraints: 805 Sorted by residual: chirality pdb=" C2 LBN B 303 " pdb=" C1 LBN B 303 " pdb=" C3 LBN B 303 " pdb=" O7 LBN B 303 " both_signs ideal model delta sigma weight residual False -2.36 2.56 -4.92 2.00e-01 2.50e+01 6.06e+02 chirality pdb=" C2 LBN A 303 " pdb=" C1 LBN A 303 " pdb=" C3 LBN A 303 " pdb=" O7 LBN A 303 " both_signs ideal model delta sigma weight residual False -2.36 2.55 -4.92 2.00e-01 2.50e+01 6.04e+02 chirality pdb=" C14 CLR A 302 " pdb=" C13 CLR A 302 " pdb=" C15 CLR A 302 " pdb=" C8 CLR A 302 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 3.97e+00 ... (remaining 802 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 145 " -0.060 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO B 146 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 13 " -0.054 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO C 14 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 94 " -0.042 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO D 95 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " -0.036 5.00e-02 4.00e+02 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 71 2.68 - 3.23: 4609 3.23 - 3.79: 7701 3.79 - 4.34: 10686 4.34 - 4.90: 18018 Nonbonded interactions: 41085 Sorted by model distance: nonbonded pdb=" OE1 GLN A 44 " pdb="ZN ZN A 301 " model vdw 2.120 2.230 nonbonded pdb=" OE1 GLN B 44 " pdb="ZN ZN B 301 " model vdw 2.172 2.230 nonbonded pdb=" NH2 ARG D 61 " pdb=" OE2 GLU D 81 " model vdw 2.356 2.520 nonbonded pdb=" NH2 ARG A 108 " pdb=" O PRO A 116 " model vdw 2.413 2.520 nonbonded pdb=" O HIS D 90 " pdb=" ND1 HIS D 90 " model vdw 2.433 2.520 ... (remaining 41080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.450 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.510 Find NCS groups from input model: 0.160 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 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 : 0.014 0.107 5237 Z= 0.930 Angle : 1.851 14.605 7105 Z= 1.350 Chirality : 0.259 4.923 805 Planarity : 0.006 0.091 848 Dihedral : 16.958 152.400 1982 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.78 % Favored : 93.90 % Rotamer: Outliers : 0.93 % Allowed : 6.16 % Favored : 92.91 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.31), residues: 623 helix: -1.21 (0.25), residues: 313 sheet: -1.44 (0.49), residues: 86 loop : -1.32 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 151 HIS 0.007 0.002 HIS D 90 PHE 0.019 0.002 PHE B 43 TYR 0.043 0.003 TYR D 49 ARG 0.003 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.570 Fit side-chains REVERT: A 137 GLU cc_start: 0.6864 (tp30) cc_final: 0.6262 (mm-30) REVERT: A 198 ARG cc_start: 0.6886 (ttm170) cc_final: 0.6588 (ttp80) REVERT: B 62 MET cc_start: 0.6309 (mtt) cc_final: 0.6034 (mtm) REVERT: B 184 ILE cc_start: 0.7178 (mm) cc_final: 0.6907 (mt) REVERT: C 10 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7500 (mp0) REVERT: C 28 THR cc_start: 0.8525 (m) cc_final: 0.8298 (t) REVERT: C 32 TYR cc_start: 0.8080 (m-80) cc_final: 0.7604 (m-80) REVERT: C 34 MET cc_start: 0.8066 (mmm) cc_final: 0.7480 (tpt) REVERT: D 30 TYR cc_start: 0.8035 (m-80) cc_final: 0.7673 (m-80) REVERT: D 71 TYR cc_start: 0.7538 (m-80) cc_final: 0.7100 (m-80) REVERT: D 100 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7906 (tp30) outliers start: 5 outliers final: 4 residues processed: 92 average time/residue: 0.2175 time to fit residues: 24.5250 Evaluate side-chains 79 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 PRO Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain D residue 90 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 95 HIS B 113 ASN B 186 HIS D 6 GLN D 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5237 Z= 0.189 Angle : 0.619 7.686 7105 Z= 0.320 Chirality : 0.041 0.177 805 Planarity : 0.005 0.076 848 Dihedral : 16.445 147.323 890 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.31 % Allowed : 11.38 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.31 (0.34), residues: 623 helix: 1.32 (0.28), residues: 316 sheet: -0.88 (0.47), residues: 116 loop : -0.82 (0.49), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.017 0.002 PHE A 39 TYR 0.012 0.001 TYR D 49 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.529 Fit side-chains REVERT: A 13 ILE cc_start: 0.6822 (mt) cc_final: 0.6602 (mt) REVERT: A 112 GLU cc_start: 0.6159 (tt0) cc_final: 0.5858 (tt0) REVERT: A 137 GLU cc_start: 0.6896 (tp30) cc_final: 0.6214 (mm-30) REVERT: B 27 LYS cc_start: 0.7386 (mmmt) cc_final: 0.6806 (mtmt) REVERT: B 62 MET cc_start: 0.6104 (mtt) cc_final: 0.5865 (mtm) REVERT: B 184 ILE cc_start: 0.6984 (mm) cc_final: 0.6755 (mt) REVERT: B 198 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7772 (mtp85) REVERT: C 62 GLN cc_start: 0.8238 (mm-40) cc_final: 0.8037 (mm-40) REVERT: D 4 MET cc_start: 0.7998 (mmm) cc_final: 0.7593 (mtp) REVERT: D 17 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7929 (mt-10) REVERT: D 30 TYR cc_start: 0.8171 (m-80) cc_final: 0.7676 (m-80) REVERT: D 90 HIS cc_start: 0.8666 (OUTLIER) cc_final: 0.8221 (p-80) REVERT: D 106 ILE cc_start: 0.7613 (pt) cc_final: 0.7381 (mt) outliers start: 7 outliers final: 3 residues processed: 90 average time/residue: 0.2133 time to fit residues: 23.7710 Evaluate side-chains 80 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.0570 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5237 Z= 0.177 Angle : 0.563 6.095 7105 Z= 0.284 Chirality : 0.040 0.200 805 Planarity : 0.005 0.076 848 Dihedral : 14.256 139.374 883 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.68 % Allowed : 13.43 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.35), residues: 623 helix: 2.24 (0.29), residues: 308 sheet: -0.71 (0.50), residues: 110 loop : -0.87 (0.47), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.015 0.001 PHE B 70 TYR 0.013 0.001 TYR D 49 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.586 Fit side-chains REVERT: A 13 ILE cc_start: 0.6900 (mt) cc_final: 0.6657 (mt) REVERT: A 27 LYS cc_start: 0.7793 (tmmt) cc_final: 0.7305 (tptt) REVERT: A 88 ARG cc_start: 0.7531 (mtp-110) cc_final: 0.7195 (mmm-85) REVERT: A 112 GLU cc_start: 0.5610 (tt0) cc_final: 0.5363 (tt0) REVERT: A 137 GLU cc_start: 0.6945 (tp30) cc_final: 0.6112 (mm-30) REVERT: B 27 LYS cc_start: 0.7435 (mmmt) cc_final: 0.6980 (ttpt) REVERT: B 62 MET cc_start: 0.6171 (mtt) cc_final: 0.5948 (mtm) REVERT: C 5 GLN cc_start: 0.7658 (tt0) cc_final: 0.7270 (tt0) outliers start: 9 outliers final: 4 residues processed: 83 average time/residue: 0.2216 time to fit residues: 23.0538 Evaluate side-chains 80 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.6993 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5237 Z= 0.312 Angle : 0.641 6.666 7105 Z= 0.327 Chirality : 0.044 0.200 805 Planarity : 0.005 0.083 848 Dihedral : 13.650 159.925 881 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.99 % Allowed : 12.13 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.86 (0.35), residues: 623 helix: 2.03 (0.29), residues: 307 sheet: -0.89 (0.47), residues: 125 loop : -0.75 (0.50), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.006 0.002 HIS D 90 PHE 0.022 0.002 PHE D 91 TYR 0.018 0.002 TYR D 49 ARG 0.002 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 88 ARG cc_start: 0.7534 (mtp-110) cc_final: 0.7189 (mmm-85) REVERT: A 112 GLU cc_start: 0.5793 (tt0) cc_final: 0.5525 (tt0) REVERT: A 137 GLU cc_start: 0.7110 (tp30) cc_final: 0.6250 (mm-30) REVERT: B 27 LYS cc_start: 0.7456 (mmmt) cc_final: 0.6986 (ttpt) REVERT: B 62 MET cc_start: 0.6195 (mtt) cc_final: 0.5932 (mtm) REVERT: B 138 MET cc_start: 0.7511 (mtp) cc_final: 0.7301 (mtt) REVERT: C 5 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7277 (tt0) REVERT: C 32 TYR cc_start: 0.8364 (m-80) cc_final: 0.8130 (m-80) REVERT: D 83 PHE cc_start: 0.8931 (m-80) cc_final: 0.8703 (m-80) outliers start: 16 outliers final: 9 residues processed: 76 average time/residue: 0.2094 time to fit residues: 20.0575 Evaluate side-chains 78 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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: 0.6971 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5237 Z= 0.248 Angle : 0.579 6.517 7105 Z= 0.295 Chirality : 0.041 0.198 805 Planarity : 0.005 0.081 848 Dihedral : 12.969 162.914 881 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.43 % Allowed : 14.37 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.97 (0.36), residues: 623 helix: 2.20 (0.29), residues: 307 sheet: -0.83 (0.48), residues: 122 loop : -0.88 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.005 0.001 HIS C 35 PHE 0.016 0.001 PHE D 91 TYR 0.015 0.001 TYR D 49 ARG 0.004 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 13 ILE cc_start: 0.6898 (mt) cc_final: 0.6623 (mt) REVERT: A 27 LYS cc_start: 0.7842 (tmmt) cc_final: 0.7272 (tptt) REVERT: A 88 ARG cc_start: 0.7537 (mtp-110) cc_final: 0.7249 (mmm-85) REVERT: A 112 GLU cc_start: 0.5740 (tt0) cc_final: 0.5492 (tt0) REVERT: A 137 GLU cc_start: 0.7052 (tp30) cc_final: 0.6359 (mm-30) REVERT: B 27 LYS cc_start: 0.7431 (mmmt) cc_final: 0.6954 (ttpt) REVERT: C 5 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: D 61 ARG cc_start: 0.7656 (ptt90) cc_final: 0.7053 (mtm180) outliers start: 13 outliers final: 12 residues processed: 80 average time/residue: 0.2140 time to fit residues: 21.2393 Evaluate side-chains 83 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 1 ASP Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5237 Z= 0.210 Angle : 0.549 6.056 7105 Z= 0.278 Chirality : 0.040 0.198 805 Planarity : 0.005 0.081 848 Dihedral : 12.604 167.170 881 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.61 % Allowed : 14.18 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.36), residues: 623 helix: 2.38 (0.29), residues: 307 sheet: -0.78 (0.48), residues: 122 loop : -0.83 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.015 0.001 PHE A 39 TYR 0.014 0.001 TYR D 49 ARG 0.002 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 13 ILE cc_start: 0.6910 (mt) cc_final: 0.6636 (mt) REVERT: A 27 LYS cc_start: 0.7852 (tmmt) cc_final: 0.7290 (tptt) REVERT: A 112 GLU cc_start: 0.5656 (tt0) cc_final: 0.5400 (tt0) REVERT: A 137 GLU cc_start: 0.7015 (tp30) cc_final: 0.6242 (mm-30) REVERT: B 13 ILE cc_start: 0.7655 (mt) cc_final: 0.7407 (mp) REVERT: B 27 LYS cc_start: 0.7433 (mmmt) cc_final: 0.6949 (ttpt) REVERT: C 5 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7292 (tt0) REVERT: D 61 ARG cc_start: 0.7575 (ptt90) cc_final: 0.7070 (mtm180) REVERT: D 74 LYS cc_start: 0.7551 (ptmm) cc_final: 0.7210 (ptmm) outliers start: 14 outliers final: 11 residues processed: 79 average time/residue: 0.2139 time to fit residues: 21.1952 Evaluate side-chains 83 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 1 ASP Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS C 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5237 Z= 0.245 Angle : 0.569 6.475 7105 Z= 0.288 Chirality : 0.041 0.198 805 Planarity : 0.005 0.084 848 Dihedral : 12.672 175.742 881 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.24 % Allowed : 14.93 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.36), residues: 623 helix: 2.32 (0.29), residues: 307 sheet: -0.68 (0.49), residues: 122 loop : -0.81 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.016 0.002 PHE D 91 TYR 0.014 0.001 TYR D 49 ARG 0.004 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 13 ILE cc_start: 0.6915 (mt) cc_final: 0.6637 (mt) REVERT: A 27 LYS cc_start: 0.7865 (tmmt) cc_final: 0.7291 (tptt) REVERT: A 112 GLU cc_start: 0.5708 (tt0) cc_final: 0.5454 (tt0) REVERT: A 137 GLU cc_start: 0.6945 (tp30) cc_final: 0.6229 (mm-30) REVERT: B 27 LYS cc_start: 0.7435 (mmmt) cc_final: 0.6944 (ttpt) REVERT: C 5 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: D 61 ARG cc_start: 0.7611 (ptt90) cc_final: 0.7083 (mtm180) REVERT: D 74 LYS cc_start: 0.7562 (ptmm) cc_final: 0.7183 (ptmm) outliers start: 12 outliers final: 11 residues processed: 78 average time/residue: 0.2250 time to fit residues: 21.7750 Evaluate side-chains 81 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 1 ASP Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.0170 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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: 0.6942 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5237 Z= 0.177 Angle : 0.528 5.975 7105 Z= 0.267 Chirality : 0.039 0.194 805 Planarity : 0.005 0.080 848 Dihedral : 12.202 177.821 881 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.24 % Allowed : 15.30 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.36), residues: 623 helix: 2.45 (0.29), residues: 310 sheet: -0.33 (0.52), residues: 108 loop : -1.16 (0.47), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.005 0.001 HIS B 182 PHE 0.014 0.001 PHE A 39 TYR 0.013 0.001 TYR D 49 ARG 0.007 0.001 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 13 ILE cc_start: 0.6985 (mt) cc_final: 0.6714 (mt) REVERT: A 27 LYS cc_start: 0.7855 (tmmt) cc_final: 0.7277 (tptt) REVERT: A 88 ARG cc_start: 0.7679 (mmm-85) cc_final: 0.7420 (mtp-110) REVERT: A 112 GLU cc_start: 0.5532 (tt0) cc_final: 0.5298 (tt0) REVERT: A 137 GLU cc_start: 0.6903 (tp30) cc_final: 0.6186 (mm-30) REVERT: B 13 ILE cc_start: 0.7685 (mt) cc_final: 0.7440 (mp) REVERT: B 27 LYS cc_start: 0.7406 (mmmt) cc_final: 0.6920 (ttpt) REVERT: B 62 MET cc_start: 0.6140 (mtt) cc_final: 0.5617 (ttm) REVERT: C 5 GLN cc_start: 0.7592 (tt0) cc_final: 0.7298 (tt0) REVERT: C 32 TYR cc_start: 0.8006 (m-80) cc_final: 0.7623 (m-80) REVERT: D 30 TYR cc_start: 0.8328 (m-80) cc_final: 0.7854 (m-10) REVERT: D 61 ARG cc_start: 0.7537 (ptt90) cc_final: 0.7105 (mtm180) REVERT: D 74 LYS cc_start: 0.7573 (ptmm) cc_final: 0.7195 (ptmm) outliers start: 12 outliers final: 12 residues processed: 81 average time/residue: 0.2129 time to fit residues: 21.6890 Evaluate side-chains 83 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 1 ASP Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5237 Z= 0.187 Angle : 0.535 6.527 7105 Z= 0.270 Chirality : 0.039 0.194 805 Planarity : 0.005 0.081 848 Dihedral : 11.883 177.709 881 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.43 % Allowed : 15.49 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.36), residues: 623 helix: 2.51 (0.29), residues: 310 sheet: -0.59 (0.49), residues: 122 loop : -0.96 (0.49), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.014 0.001 PHE A 39 TYR 0.013 0.001 TYR D 49 ARG 0.006 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 13 ILE cc_start: 0.6988 (mt) cc_final: 0.6716 (mt) REVERT: A 27 LYS cc_start: 0.7928 (tmmt) cc_final: 0.7326 (tptt) REVERT: A 88 ARG cc_start: 0.7670 (mmm-85) cc_final: 0.7449 (mtp-110) REVERT: A 112 GLU cc_start: 0.5540 (tt0) cc_final: 0.5298 (tt0) REVERT: A 137 GLU cc_start: 0.6900 (tp30) cc_final: 0.6207 (mm-30) REVERT: A 189 MET cc_start: 0.7428 (tpt) cc_final: 0.7219 (tpt) REVERT: B 13 ILE cc_start: 0.7668 (mt) cc_final: 0.7421 (mp) REVERT: B 27 LYS cc_start: 0.7411 (mmmt) cc_final: 0.6921 (ttpt) REVERT: B 62 MET cc_start: 0.6115 (mtt) cc_final: 0.5605 (ttm) REVERT: C 5 GLN cc_start: 0.7575 (tt0) cc_final: 0.7297 (tt0) REVERT: C 32 TYR cc_start: 0.7973 (m-80) cc_final: 0.7601 (m-80) REVERT: D 30 TYR cc_start: 0.8326 (m-80) cc_final: 0.7843 (m-10) REVERT: D 61 ARG cc_start: 0.7500 (ptt90) cc_final: 0.7130 (mtm180) REVERT: D 74 LYS cc_start: 0.7591 (ptmm) cc_final: 0.7217 (ptmm) outliers start: 13 outliers final: 13 residues processed: 78 average time/residue: 0.2140 time to fit residues: 20.8118 Evaluate side-chains 81 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 1 ASP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 0.0970 chunk 7 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5237 Z= 0.200 Angle : 0.538 6.076 7105 Z= 0.272 Chirality : 0.040 0.193 805 Planarity : 0.005 0.082 848 Dihedral : 11.703 173.708 881 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.43 % Allowed : 15.67 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.36), residues: 623 helix: 2.56 (0.29), residues: 307 sheet: -0.60 (0.49), residues: 122 loop : -0.86 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.015 0.001 PHE A 39 TYR 0.013 0.001 TYR D 49 ARG 0.006 0.000 ARG A 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7016 (mt) cc_final: 0.6744 (mt) REVERT: A 27 LYS cc_start: 0.7938 (tmmt) cc_final: 0.7323 (tptt) REVERT: A 112 GLU cc_start: 0.5696 (tt0) cc_final: 0.5454 (tt0) REVERT: A 137 GLU cc_start: 0.6893 (tp30) cc_final: 0.6188 (mm-30) REVERT: A 189 MET cc_start: 0.7437 (tpt) cc_final: 0.7221 (tpt) REVERT: B 13 ILE cc_start: 0.7679 (mt) cc_final: 0.7433 (mp) REVERT: B 27 LYS cc_start: 0.7412 (mmmt) cc_final: 0.6920 (ttpt) REVERT: B 62 MET cc_start: 0.6119 (mtt) cc_final: 0.5663 (ttm) REVERT: C 5 GLN cc_start: 0.7577 (tt0) cc_final: 0.7326 (tt0) REVERT: C 32 TYR cc_start: 0.7981 (m-80) cc_final: 0.7614 (m-80) REVERT: D 30 TYR cc_start: 0.8341 (m-80) cc_final: 0.7850 (m-10) REVERT: D 61 ARG cc_start: 0.7523 (ptt90) cc_final: 0.7152 (mtm180) REVERT: D 74 LYS cc_start: 0.7593 (ptmm) cc_final: 0.7214 (ptmm) outliers start: 13 outliers final: 12 residues processed: 76 average time/residue: 0.2143 time to fit residues: 20.2568 Evaluate side-chains 80 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 1 ASP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.174844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.143821 restraints weight = 5958.689| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.12 r_work: 0.3524 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5237 Z= 0.196 Angle : 0.535 6.284 7105 Z= 0.270 Chirality : 0.039 0.193 805 Planarity : 0.005 0.081 848 Dihedral : 11.601 172.371 881 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.43 % Allowed : 15.67 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.36), residues: 623 helix: 2.54 (0.29), residues: 308 sheet: -0.62 (0.48), residues: 122 loop : -0.93 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.014 0.001 PHE A 39 TYR 0.013 0.001 TYR D 49 ARG 0.004 0.000 ARG C 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1525.83 seconds wall clock time: 27 minutes 47.07 seconds (1667.07 seconds total)