Starting phenix.real_space_refine on Mon Sep 23 19:37:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/09_2024/7p2q_13172_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/09_2024/7p2q_13172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/09_2024/7p2q_13172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/09_2024/7p2q_13172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/09_2024/7p2q_13172_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/09_2024/7p2q_13172_neut.cif" } resolution = 4.9 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= 0.002 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 23 5.16 5 C 3106 2.51 5 N 778 2.21 5 O 873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4780 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain: "B" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1426 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "C" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1411 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "D" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 696 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: 3.37, per 1000 atoms: 0.71 Number of scatterers: 4780 At special positions: 0 Unit cell: (81.81, 84.24, 126.36, 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 23 16.00 O 873 8.00 N 778 7.00 C 3106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG E 1 " - " ASN B 141 " Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 572.3 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 6 sheets defined 41.4% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 26 through 56 removed outlier: 4.288A pdb=" N LEU A 30 " --> pdb=" O ASN A 26 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.782A pdb=" N VAL A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 33 Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 79 through 105 Processing helix chain 'C' and resid 106 through 109 removed outlier: 3.516A pdb=" N GLU C 109 " --> pdb=" O PRO C 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 106 through 109' Processing helix chain 'C' and resid 110 through 136 removed outlier: 3.720A pdb=" N LEU C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 207 through 224 removed outlier: 3.700A pdb=" N GLU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.653A pdb=" N LEU D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 109 Processing helix chain 'D' and resid 112 through 131 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 140 through 145 removed outlier: 3.601A pdb=" N LEU D 145 " --> pdb=" O PRO D 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 3.983A pdb=" N ASP A 77 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 99 removed outlier: 5.282A pdb=" N VAL A 110 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS A 126 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 112 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.094A pdb=" N VAL B 51 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 63 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP B 53 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER B 61 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 129 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.679A pdb=" N GLN B 84 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 104 Processing sheet with id=AA6, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.622A pdb=" N LEU C 159 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL C 142 " --> pdb=" O TRP C 157 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TRP C 157 " --> pdb=" O VAL C 142 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 693 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: 1.12 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1460 1.34 - 1.46: 971 1.46 - 1.58: 2424 1.58 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 4896 Sorted by residual: bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.567 -0.048 2.00e-02 2.50e+03 5.76e+00 bond pdb=" C1 MAN E 4 " pdb=" C2 MAN E 4 " ideal model delta sigma weight residual 1.526 1.563 -0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" C1 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sigma weight residual 1.410 1.445 -0.035 2.00e-02 2.50e+03 2.99e+00 bond pdb=" C5 MAN E 4 " pdb=" O5 MAN E 4 " ideal model delta sigma weight residual 1.418 1.452 -0.034 2.00e-02 2.50e+03 2.94e+00 bond pdb=" C LEU D 131 " pdb=" N PRO D 132 " ideal model delta sigma weight residual 1.329 1.349 -0.020 1.18e-02 7.18e+03 2.88e+00 ... (remaining 4891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 6412 1.91 - 3.81: 165 3.81 - 5.72: 31 5.72 - 7.63: 15 7.63 - 9.53: 6 Bond angle restraints: 6629 Sorted by residual: angle pdb=" C LYS B 121 " pdb=" N ASP B 122 " pdb=" CA ASP B 122 " ideal model delta sigma weight residual 121.54 131.00 -9.46 1.91e+00 2.74e-01 2.45e+01 angle pdb=" C GLY B 133 " pdb=" N ASN B 134 " pdb=" CA ASN B 134 " ideal model delta sigma weight residual 121.54 130.70 -9.16 1.91e+00 2.74e-01 2.30e+01 angle pdb=" C GLU A 58 " pdb=" N SER A 59 " pdb=" CA SER A 59 " ideal model delta sigma weight residual 121.80 130.19 -8.39 2.44e+00 1.68e-01 1.18e+01 angle pdb=" N SER A 59 " pdb=" CA SER A 59 " pdb=" C SER A 59 " ideal model delta sigma weight residual 109.81 116.82 -7.01 2.21e+00 2.05e-01 1.00e+01 angle pdb=" CA LEU D 75 " pdb=" CB LEU D 75 " pdb=" CG LEU D 75 " ideal model delta sigma weight residual 116.30 125.83 -9.53 3.50e+00 8.16e-02 7.42e+00 ... (remaining 6624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.22: 2892 21.22 - 42.44: 61 42.44 - 63.66: 4 63.66 - 84.89: 7 84.89 - 106.11: 4 Dihedral angle restraints: 2968 sinusoidal: 1260 harmonic: 1708 Sorted by residual: dihedral pdb=" CA ASP C 154 " pdb=" C ASP C 154 " pdb=" N ASP C 155 " pdb=" CA ASP C 155 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA TYR B 174 " pdb=" C TYR B 174 " pdb=" N GLU B 175 " pdb=" CA GLU B 175 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.40 106.11 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 2965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 590 0.057 - 0.114: 138 0.114 - 0.171: 22 0.171 - 0.228: 5 0.228 - 0.285: 1 Chirality restraints: 756 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE B 109 " pdb=" CA ILE B 109 " pdb=" CG1 ILE B 109 " pdb=" CG2 ILE B 109 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASN B 134 " pdb=" N ASN B 134 " pdb=" C ASN B 134 " pdb=" CB ASN B 134 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 753 not shown) Planarity restraints: 822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 140 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO D 141 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 70 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A 71 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 37 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 38 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " -0.026 5.00e-02 4.00e+02 ... (remaining 819 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1005 2.79 - 3.32: 4108 3.32 - 3.85: 7306 3.85 - 4.37: 7850 4.37 - 4.90: 13680 Nonbonded interactions: 33949 Sorted by model distance: nonbonded pdb=" NH1 ARG A 109 " pdb=" CE1 PHE B 86 " model vdw 2.264 3.420 nonbonded pdb=" O LYS B 121 " pdb=" OD1 ASP B 122 " model vdw 2.290 3.040 nonbonded pdb=" NH1 ARG C 84 " pdb=" OE2 GLU C 136 " model vdw 2.352 3.120 nonbonded pdb=" OG SER B 90 " pdb=" O THR B 145 " model vdw 2.357 3.040 nonbonded pdb=" OD1 ASP A 120 " pdb=" NZ LYS A 147 " model vdw 2.401 3.120 ... (remaining 33944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.220 Find NCS groups from input model: 0.050 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4896 Z= 0.243 Angle : 0.840 9.532 6629 Z= 0.432 Chirality : 0.051 0.285 756 Planarity : 0.007 0.057 821 Dihedral : 11.107 106.107 1866 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.29), residues: 579 helix: -1.26 (0.24), residues: 220 sheet: -1.18 (0.47), residues: 120 loop : -3.26 (0.32), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 157 HIS 0.009 0.002 HIS C 144 PHE 0.024 0.002 PHE A 80 TYR 0.023 0.002 TYR B 174 ARG 0.005 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8489 (m-10) cc_final: 0.7727 (m-80) REVERT: A 47 ILE cc_start: 0.8986 (mt) cc_final: 0.8784 (mt) REVERT: A 52 ILE cc_start: 0.8925 (pt) cc_final: 0.8577 (pt) REVERT: A 90 ARG cc_start: 0.7608 (mtm110) cc_final: 0.7112 (mmt90) REVERT: A 134 ASP cc_start: 0.8211 (m-30) cc_final: 0.7242 (t0) REVERT: A 146 GLU cc_start: 0.6990 (tt0) cc_final: 0.6722 (tt0) REVERT: A 158 LEU cc_start: 0.8953 (mm) cc_final: 0.8742 (mm) REVERT: B 42 HIS cc_start: 0.8714 (m-70) cc_final: 0.8397 (t-170) REVERT: B 49 LYS cc_start: 0.8171 (ptmt) cc_final: 0.7918 (ptpp) REVERT: B 59 GLU cc_start: 0.7296 (tp30) cc_final: 0.6952 (tp30) REVERT: B 73 ASP cc_start: 0.8255 (t0) cc_final: 0.7370 (t70) REVERT: B 78 PHE cc_start: 0.7880 (m-80) cc_final: 0.7513 (m-80) REVERT: B 80 TRP cc_start: 0.6359 (m100) cc_final: 0.5855 (p-90) REVERT: B 128 PHE cc_start: 0.7994 (m-10) cc_final: 0.7730 (m-10) REVERT: C 70 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8536 (tm-30) REVERT: C 102 ASP cc_start: 0.8659 (m-30) cc_final: 0.8314 (m-30) REVERT: C 174 LEU cc_start: 0.8449 (mm) cc_final: 0.7380 (mm) REVERT: C 208 TYR cc_start: 0.9118 (t80) cc_final: 0.8689 (t80) REVERT: D 68 MET cc_start: 0.9152 (mtt) cc_final: 0.8800 (tmm) REVERT: D 128 LEU cc_start: 0.8645 (mt) cc_final: 0.8394 (pp) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2110 time to fit residues: 67.4959 Evaluate side-chains 153 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4896 Z= 0.209 Angle : 0.711 9.183 6629 Z= 0.360 Chirality : 0.046 0.184 756 Planarity : 0.006 0.060 821 Dihedral : 10.478 84.931 731 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.19 % Allowed : 1.34 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.33), residues: 579 helix: 0.62 (0.31), residues: 220 sheet: -0.74 (0.48), residues: 126 loop : -2.81 (0.34), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 101 HIS 0.007 0.001 HIS C 144 PHE 0.018 0.002 PHE A 37 TYR 0.018 0.002 TYR C 208 ARG 0.006 0.001 ARG C 145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.9006 (m-80) cc_final: 0.8700 (m-80) REVERT: A 32 TYR cc_start: 0.8231 (m-10) cc_final: 0.7949 (m-80) REVERT: A 33 GLN cc_start: 0.8981 (mm110) cc_final: 0.8635 (mm-40) REVERT: A 46 MET cc_start: 0.8049 (ttp) cc_final: 0.7717 (ttp) REVERT: A 121 ILE cc_start: 0.6751 (mm) cc_final: 0.5915 (mm) REVERT: A 134 ASP cc_start: 0.7679 (m-30) cc_final: 0.7446 (t0) REVERT: A 146 GLU cc_start: 0.6777 (tt0) cc_final: 0.6491 (tt0) REVERT: A 158 LEU cc_start: 0.8969 (mm) cc_final: 0.8385 (mm) REVERT: B 42 HIS cc_start: 0.8815 (m-70) cc_final: 0.8483 (t-170) REVERT: B 73 ASP cc_start: 0.8403 (t0) cc_final: 0.7538 (t70) REVERT: B 80 TRP cc_start: 0.6419 (m100) cc_final: 0.5733 (p-90) REVERT: C 94 PHE cc_start: 0.8870 (m-10) cc_final: 0.8600 (m-10) REVERT: C 102 ASP cc_start: 0.8657 (m-30) cc_final: 0.8438 (m-30) REVERT: C 174 LEU cc_start: 0.8164 (mm) cc_final: 0.7802 (mm) REVERT: C 208 TYR cc_start: 0.9088 (t80) cc_final: 0.8781 (t80) REVERT: D 131 LEU cc_start: 0.8879 (mt) cc_final: 0.8539 (mt) REVERT: D 139 ARG cc_start: 0.8374 (ttt180) cc_final: 0.8033 (ptt180) outliers start: 1 outliers final: 1 residues processed: 192 average time/residue: 0.1785 time to fit residues: 41.9960 Evaluate side-chains 138 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4896 Z= 0.167 Angle : 0.663 7.494 6629 Z= 0.332 Chirality : 0.045 0.220 756 Planarity : 0.004 0.048 821 Dihedral : 9.640 76.110 731 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.34), residues: 579 helix: 1.20 (0.33), residues: 225 sheet: -0.10 (0.49), residues: 125 loop : -2.76 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 148 HIS 0.006 0.001 HIS D 71 PHE 0.015 0.001 PHE A 37 TYR 0.018 0.001 TYR C 121 ARG 0.003 0.000 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.9005 (m-80) cc_final: 0.8701 (m-80) REVERT: A 32 TYR cc_start: 0.8263 (m-10) cc_final: 0.8026 (m-80) REVERT: A 33 GLN cc_start: 0.9048 (mm110) cc_final: 0.8683 (mm-40) REVERT: A 46 MET cc_start: 0.8022 (ttp) cc_final: 0.7494 (ttp) REVERT: A 74 HIS cc_start: 0.8637 (m-70) cc_final: 0.8097 (m-70) REVERT: A 121 ILE cc_start: 0.6955 (mm) cc_final: 0.6540 (mm) REVERT: A 133 ASP cc_start: 0.6967 (t70) cc_final: 0.6460 (t70) REVERT: A 134 ASP cc_start: 0.7751 (m-30) cc_final: 0.7361 (t0) REVERT: A 146 GLU cc_start: 0.6682 (tt0) cc_final: 0.6471 (tt0) REVERT: B 42 HIS cc_start: 0.8762 (m-70) cc_final: 0.8434 (t-170) REVERT: B 73 ASP cc_start: 0.8405 (t0) cc_final: 0.8103 (m-30) REVERT: B 80 TRP cc_start: 0.6427 (m100) cc_final: 0.5614 (p-90) REVERT: C 94 PHE cc_start: 0.8973 (m-10) cc_final: 0.8660 (m-10) REVERT: C 102 ASP cc_start: 0.8615 (m-30) cc_final: 0.8379 (m-30) REVERT: C 121 TYR cc_start: 0.8273 (t80) cc_final: 0.7863 (t80) REVERT: C 162 SER cc_start: 0.8240 (t) cc_final: 0.8004 (t) REVERT: C 167 ASP cc_start: 0.8244 (t0) cc_final: 0.7758 (t0) REVERT: C 168 ASP cc_start: 0.8385 (t0) cc_final: 0.7953 (t0) REVERT: C 208 TYR cc_start: 0.9021 (t80) cc_final: 0.8668 (t80) REVERT: D 71 HIS cc_start: 0.7355 (m90) cc_final: 0.6954 (m-70) REVERT: D 139 ARG cc_start: 0.8361 (ttt180) cc_final: 0.8039 (ptt180) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1585 time to fit residues: 35.3382 Evaluate side-chains 147 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 24 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4896 Z= 0.200 Angle : 0.689 7.971 6629 Z= 0.344 Chirality : 0.045 0.197 756 Planarity : 0.004 0.041 821 Dihedral : 8.858 66.473 731 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.35), residues: 579 helix: 1.51 (0.34), residues: 225 sheet: -0.16 (0.50), residues: 130 loop : -2.65 (0.35), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 148 HIS 0.003 0.001 HIS C 199 PHE 0.013 0.002 PHE A 37 TYR 0.019 0.001 TYR B 88 ARG 0.004 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.9049 (m-80) cc_final: 0.8705 (m-80) REVERT: A 32 TYR cc_start: 0.8273 (m-10) cc_final: 0.7990 (m-80) REVERT: A 33 GLN cc_start: 0.9045 (mm110) cc_final: 0.8659 (mm110) REVERT: A 46 MET cc_start: 0.8055 (ttp) cc_final: 0.7573 (ttp) REVERT: A 112 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8589 (mmmm) REVERT: B 42 HIS cc_start: 0.8800 (m-70) cc_final: 0.8452 (m-70) REVERT: B 47 MET cc_start: 0.6900 (tmm) cc_final: 0.6657 (tmm) REVERT: B 122 ASP cc_start: 0.8836 (p0) cc_final: 0.8627 (p0) REVERT: C 70 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8349 (tm-30) REVERT: C 94 PHE cc_start: 0.8810 (m-10) cc_final: 0.8539 (m-10) REVERT: C 102 ASP cc_start: 0.8661 (m-30) cc_final: 0.8451 (m-30) REVERT: C 124 MET cc_start: 0.7417 (ppp) cc_final: 0.7177 (ptt) REVERT: C 167 ASP cc_start: 0.8097 (t0) cc_final: 0.7638 (t0) REVERT: C 208 TYR cc_start: 0.9040 (t80) cc_final: 0.8731 (t80) REVERT: D 139 ARG cc_start: 0.8438 (ttt180) cc_final: 0.8097 (ptt180) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1653 time to fit residues: 35.8041 Evaluate side-chains 135 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.0570 chunk 46 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4896 Z= 0.156 Angle : 0.678 8.676 6629 Z= 0.329 Chirality : 0.045 0.200 756 Planarity : 0.004 0.041 821 Dihedral : 8.141 56.255 731 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.35), residues: 579 helix: 1.69 (0.35), residues: 226 sheet: 0.32 (0.49), residues: 129 loop : -2.58 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 148 HIS 0.003 0.001 HIS C 216 PHE 0.020 0.001 PHE C 197 TYR 0.014 0.001 TYR B 88 ARG 0.003 0.000 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8249 (m-10) cc_final: 0.8012 (m-80) REVERT: A 46 MET cc_start: 0.7988 (ttp) cc_final: 0.7549 (ttp) REVERT: A 93 GLU cc_start: 0.6240 (pm20) cc_final: 0.5932 (pm20) REVERT: A 146 GLU cc_start: 0.6460 (tt0) cc_final: 0.6072 (tt0) REVERT: B 42 HIS cc_start: 0.8684 (m-70) cc_final: 0.8412 (t70) REVERT: B 49 LYS cc_start: 0.7195 (mttp) cc_final: 0.6449 (mtmm) REVERT: B 122 ASP cc_start: 0.8843 (p0) cc_final: 0.8623 (p0) REVERT: C 94 PHE cc_start: 0.8865 (m-10) cc_final: 0.8612 (m-10) REVERT: C 102 ASP cc_start: 0.8592 (m-30) cc_final: 0.8360 (m-30) REVERT: C 166 PHE cc_start: 0.6961 (m-10) cc_final: 0.6171 (m-10) REVERT: C 167 ASP cc_start: 0.7822 (t0) cc_final: 0.7332 (t0) REVERT: C 174 LEU cc_start: 0.8421 (mm) cc_final: 0.7921 (mp) REVERT: C 208 TYR cc_start: 0.9071 (t80) cc_final: 0.8695 (t80) REVERT: D 68 MET cc_start: 0.8390 (ptp) cc_final: 0.7934 (tmm) REVERT: D 71 HIS cc_start: 0.7538 (m90) cc_final: 0.7248 (m90) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1512 time to fit residues: 33.6370 Evaluate side-chains 136 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 HIS A 114 HIS A 129 ASN C 58 ASN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 4896 Z= 0.375 Angle : 0.863 10.773 6629 Z= 0.442 Chirality : 0.049 0.211 756 Planarity : 0.005 0.048 821 Dihedral : 7.839 55.530 731 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.35), residues: 579 helix: 1.00 (0.33), residues: 219 sheet: -0.06 (0.54), residues: 114 loop : -2.41 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 134 HIS 0.011 0.003 HIS D 140 PHE 0.021 0.003 PHE A 84 TYR 0.021 0.003 TYR B 88 ARG 0.008 0.001 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8129 (m-10) cc_final: 0.7874 (m-80) REVERT: A 33 GLN cc_start: 0.9054 (mm110) cc_final: 0.8735 (mm110) REVERT: A 46 MET cc_start: 0.7957 (ttp) cc_final: 0.7636 (ttp) REVERT: A 69 MET cc_start: 0.9457 (mmm) cc_final: 0.9204 (mmm) REVERT: A 112 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8687 (mmmt) REVERT: A 128 ASP cc_start: 0.8777 (t0) cc_final: 0.8535 (t0) REVERT: A 146 GLU cc_start: 0.6511 (tt0) cc_final: 0.5922 (tt0) REVERT: A 158 LEU cc_start: 0.9207 (mm) cc_final: 0.8765 (mm) REVERT: B 42 HIS cc_start: 0.8827 (m-70) cc_final: 0.8510 (m-70) REVERT: B 86 PHE cc_start: 0.7984 (m-80) cc_final: 0.7763 (m-80) REVERT: B 122 ASP cc_start: 0.8911 (p0) cc_final: 0.8665 (p0) REVERT: C 102 ASP cc_start: 0.8752 (m-30) cc_final: 0.8507 (m-30) REVERT: C 121 TYR cc_start: 0.8270 (t80) cc_final: 0.7680 (t80) REVERT: C 188 GLU cc_start: 0.8916 (pp20) cc_final: 0.8542 (pp20) REVERT: C 208 TYR cc_start: 0.9009 (t80) cc_final: 0.8727 (t80) REVERT: D 68 MET cc_start: 0.8462 (ptp) cc_final: 0.8035 (tmm) REVERT: D 71 HIS cc_start: 0.7449 (m90) cc_final: 0.7223 (m90) REVERT: D 139 ARG cc_start: 0.7963 (tmm160) cc_final: 0.7722 (ttp80) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1458 time to fit residues: 29.6232 Evaluate side-chains 124 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4896 Z= 0.225 Angle : 0.733 12.073 6629 Z= 0.362 Chirality : 0.044 0.157 756 Planarity : 0.004 0.038 821 Dihedral : 6.678 55.792 731 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.35), residues: 579 helix: 1.50 (0.34), residues: 219 sheet: -0.39 (0.48), residues: 130 loop : -2.27 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 144 HIS 0.004 0.001 HIS C 216 PHE 0.028 0.002 PHE C 94 TYR 0.018 0.002 TYR B 88 ARG 0.003 0.001 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.9047 (m-80) cc_final: 0.8669 (m-80) REVERT: A 32 TYR cc_start: 0.8193 (m-10) cc_final: 0.7972 (m-80) REVERT: A 69 MET cc_start: 0.9454 (mmm) cc_final: 0.9208 (mmm) REVERT: A 112 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8710 (mmmt) REVERT: A 128 ASP cc_start: 0.8928 (t0) cc_final: 0.8674 (t0) REVERT: A 146 GLU cc_start: 0.6539 (tt0) cc_final: 0.5924 (tt0) REVERT: B 42 HIS cc_start: 0.8789 (m-70) cc_final: 0.8490 (m-70) REVERT: B 49 LYS cc_start: 0.7341 (mttt) cc_final: 0.7135 (mttp) REVERT: B 65 PHE cc_start: 0.8653 (m-80) cc_final: 0.8441 (m-10) REVERT: B 88 TYR cc_start: 0.7322 (m-80) cc_final: 0.6462 (m-10) REVERT: B 122 ASP cc_start: 0.8891 (p0) cc_final: 0.8632 (p0) REVERT: C 102 ASP cc_start: 0.8686 (m-30) cc_final: 0.8427 (m-30) REVERT: C 188 GLU cc_start: 0.8889 (pp20) cc_final: 0.8582 (pp20) REVERT: C 208 TYR cc_start: 0.8990 (t80) cc_final: 0.8718 (t80) REVERT: D 68 MET cc_start: 0.8589 (ptp) cc_final: 0.8075 (tmm) REVERT: D 71 HIS cc_start: 0.7468 (m90) cc_final: 0.7199 (m-70) REVERT: D 139 ARG cc_start: 0.7899 (tmm160) cc_final: 0.7674 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1449 time to fit residues: 30.9746 Evaluate side-chains 125 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 21 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.7123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4896 Z= 0.173 Angle : 0.708 10.897 6629 Z= 0.347 Chirality : 0.045 0.193 756 Planarity : 0.004 0.035 821 Dihedral : 6.018 56.042 731 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.35), residues: 579 helix: 1.64 (0.34), residues: 221 sheet: -0.29 (0.49), residues: 121 loop : -2.29 (0.35), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 144 HIS 0.003 0.001 HIS D 140 PHE 0.015 0.002 PHE D 123 TYR 0.011 0.001 TYR B 88 ARG 0.003 0.000 ARG C 145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8247 (m-10) cc_final: 0.7936 (m-80) REVERT: A 121 ILE cc_start: 0.7121 (mm) cc_final: 0.6895 (mm) REVERT: A 128 ASP cc_start: 0.8914 (t0) cc_final: 0.8700 (t0) REVERT: A 146 GLU cc_start: 0.6402 (tt0) cc_final: 0.5700 (tt0) REVERT: A 158 LEU cc_start: 0.9159 (mm) cc_final: 0.8370 (mm) REVERT: B 42 HIS cc_start: 0.8688 (m-70) cc_final: 0.8392 (m-70) REVERT: B 88 TYR cc_start: 0.7277 (m-80) cc_final: 0.6385 (m-10) REVERT: B 122 ASP cc_start: 0.8889 (p0) cc_final: 0.8636 (p0) REVERT: B 128 PHE cc_start: 0.8985 (p90) cc_final: 0.8623 (p90) REVERT: B 130 PHE cc_start: 0.8572 (p90) cc_final: 0.8221 (p90) REVERT: B 144 LEU cc_start: 0.9504 (mm) cc_final: 0.9228 (tp) REVERT: C 102 ASP cc_start: 0.8629 (m-30) cc_final: 0.8356 (m-30) REVERT: C 166 PHE cc_start: 0.6944 (m-10) cc_final: 0.6123 (m-10) REVERT: C 188 GLU cc_start: 0.8889 (pp20) cc_final: 0.8648 (pp20) REVERT: C 203 LEU cc_start: 0.7826 (tp) cc_final: 0.7530 (tp) REVERT: C 208 TYR cc_start: 0.9007 (t80) cc_final: 0.8744 (t80) REVERT: D 68 MET cc_start: 0.8602 (ptp) cc_final: 0.8126 (tmm) REVERT: D 71 HIS cc_start: 0.7504 (m90) cc_final: 0.7218 (m-70) REVERT: D 139 ARG cc_start: 0.7873 (tmm160) cc_final: 0.7647 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1574 time to fit residues: 34.1749 Evaluate side-chains 129 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.7363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4896 Z= 0.232 Angle : 0.763 10.879 6629 Z= 0.375 Chirality : 0.046 0.225 756 Planarity : 0.004 0.048 821 Dihedral : 6.170 55.895 731 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.35), residues: 579 helix: 1.63 (0.35), residues: 221 sheet: -0.23 (0.48), residues: 122 loop : -2.27 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 144 HIS 0.004 0.001 HIS C 199 PHE 0.027 0.002 PHE C 197 TYR 0.015 0.002 TYR B 174 ARG 0.004 0.000 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.9059 (m-80) cc_final: 0.8708 (m-80) REVERT: A 32 TYR cc_start: 0.8277 (m-10) cc_final: 0.8065 (m-80) REVERT: A 69 MET cc_start: 0.9460 (mmm) cc_final: 0.9222 (mmm) REVERT: A 112 LYS cc_start: 0.8816 (mmtm) cc_final: 0.8562 (mmmt) REVERT: A 121 ILE cc_start: 0.7161 (mm) cc_final: 0.6911 (mm) REVERT: A 128 ASP cc_start: 0.8950 (t0) cc_final: 0.8664 (t0) REVERT: A 146 GLU cc_start: 0.6369 (tt0) cc_final: 0.5583 (tt0) REVERT: B 42 HIS cc_start: 0.8718 (m-70) cc_final: 0.8396 (m-70) REVERT: B 88 TYR cc_start: 0.7456 (m-80) cc_final: 0.6592 (m-10) REVERT: B 122 ASP cc_start: 0.8929 (p0) cc_final: 0.8661 (p0) REVERT: C 102 ASP cc_start: 0.8653 (m-30) cc_final: 0.8377 (m-30) REVERT: C 166 PHE cc_start: 0.6905 (m-10) cc_final: 0.6101 (m-10) REVERT: C 188 GLU cc_start: 0.8920 (pp20) cc_final: 0.8657 (pp20) REVERT: C 208 TYR cc_start: 0.9028 (t80) cc_final: 0.8728 (t80) REVERT: D 68 MET cc_start: 0.8593 (ptp) cc_final: 0.8032 (tmm) REVERT: D 71 HIS cc_start: 0.7499 (m90) cc_final: 0.7238 (m90) REVERT: D 85 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8634 (mmtt) REVERT: D 139 ARG cc_start: 0.7924 (tmm160) cc_final: 0.7687 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1572 time to fit residues: 31.5990 Evaluate side-chains 128 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.7525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4896 Z= 0.205 Angle : 0.768 10.936 6629 Z= 0.380 Chirality : 0.045 0.171 756 Planarity : 0.004 0.043 821 Dihedral : 6.097 56.172 731 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.35), residues: 579 helix: 1.58 (0.35), residues: 221 sheet: -0.30 (0.46), residues: 123 loop : -2.31 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 144 HIS 0.004 0.001 HIS C 199 PHE 0.015 0.002 PHE B 65 TYR 0.012 0.001 TYR B 88 ARG 0.003 0.000 ARG A 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.9051 (m-80) cc_final: 0.8698 (m-80) REVERT: A 32 TYR cc_start: 0.8262 (m-10) cc_final: 0.8058 (m-80) REVERT: A 112 LYS cc_start: 0.8834 (mmtm) cc_final: 0.8535 (mmmt) REVERT: A 121 ILE cc_start: 0.7163 (mm) cc_final: 0.6897 (mm) REVERT: A 146 GLU cc_start: 0.6371 (tt0) cc_final: 0.5872 (tt0) REVERT: A 158 LEU cc_start: 0.9169 (mm) cc_final: 0.8569 (mm) REVERT: B 42 HIS cc_start: 0.8678 (m-70) cc_final: 0.8373 (m-70) REVERT: B 88 TYR cc_start: 0.7380 (m-80) cc_final: 0.6576 (m-10) REVERT: B 122 ASP cc_start: 0.8895 (p0) cc_final: 0.8626 (p0) REVERT: B 144 LEU cc_start: 0.9525 (mm) cc_final: 0.9272 (tp) REVERT: C 102 ASP cc_start: 0.8653 (m-30) cc_final: 0.8366 (m-30) REVERT: C 188 GLU cc_start: 0.8929 (pp20) cc_final: 0.8649 (pp20) REVERT: D 68 MET cc_start: 0.8587 (ptp) cc_final: 0.8089 (tmm) REVERT: D 71 HIS cc_start: 0.7555 (m90) cc_final: 0.7273 (m-70) REVERT: D 139 ARG cc_start: 0.7923 (tmm160) cc_final: 0.7678 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1442 time to fit residues: 29.5352 Evaluate side-chains 126 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 5.9990 chunk 5 optimal weight: 0.0970 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.073587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.057856 restraints weight = 26572.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.059387 restraints weight = 20484.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.060617 restraints weight = 16657.152| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.7566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4896 Z= 0.187 Angle : 0.756 11.028 6629 Z= 0.370 Chirality : 0.045 0.169 756 Planarity : 0.004 0.041 821 Dihedral : 5.977 56.198 731 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.35), residues: 579 helix: 1.62 (0.35), residues: 221 sheet: -0.32 (0.46), residues: 124 loop : -2.27 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 144 HIS 0.003 0.001 HIS C 199 PHE 0.013 0.002 PHE A 80 TYR 0.016 0.001 TYR D 107 ARG 0.003 0.000 ARG A 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1403.10 seconds wall clock time: 25 minutes 48.08 seconds (1548.08 seconds total)