Starting phenix.real_space_refine on Wed Sep 25 11:46:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/09_2024/6m4d_30076.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/09_2024/6m4d_30076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/09_2024/6m4d_30076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/09_2024/6m4d_30076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/09_2024/6m4d_30076.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/09_2024/6m4d_30076.cif" } resolution = 4.4 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= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 250 5.49 5 S 14 5.16 5 C 5801 2.51 5 N 1962 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10497 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 693 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2548 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "J" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2577 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Restraints were copied for chains: E, F, G, H Time building chain proxies: 7.01, per 1000 atoms: 0.67 Number of scatterers: 10497 At special positions: 0 Unit cell: (131.04, 79.04, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 250 15.00 O 2470 8.00 N 1962 7.00 C 5801 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 Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 692.3 milliseconds 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1272 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 3 sheets defined 75.1% alpha, 0.9% beta 123 base pairs and 185 stacking pairs defined. Time for finding SS restraints: 5.26 Creating SS restraints... Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.724A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 18 through 24 Processing helix chain 'C' and resid 28 through 38 Processing helix chain 'C' and resid 47 through 75 Processing helix chain 'C' and resid 82 through 91 removed outlier: 3.571A pdb=" N LEU C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.723A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 18 through 24 Processing helix chain 'G' and resid 28 through 38 Processing helix chain 'G' and resid 47 through 75 Processing helix chain 'G' and resid 82 through 91 removed outlier: 3.571A pdb=" N LEU G 86 " --> pdb=" O THR G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 100 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.952A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.068A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 381 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 317 hydrogen bonds 622 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 185 stacking parallelities Total time for adding SS restraints: 3.63 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1934 1.33 - 1.45: 3674 1.45 - 1.57: 5056 1.57 - 1.68: 498 1.68 - 1.80: 24 Bond restraints: 11186 Sorted by residual: bond pdb=" P DG J 136 " pdb=" O5' DG J 136 " ideal model delta sigma weight residual 1.600 1.639 -0.039 2.00e-02 2.50e+03 3.89e+00 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.473 -0.051 3.00e-02 1.11e+03 2.85e+00 bond pdb=" C5' DG J 136 " pdb=" C4' DG J 136 " ideal model delta sigma weight residual 1.518 1.551 -0.033 2.00e-02 2.50e+03 2.66e+00 bond pdb=" C1' DC I 56 " pdb=" N1 DC I 56 " ideal model delta sigma weight residual 1.490 1.441 0.049 3.00e-02 1.11e+03 2.62e+00 bond pdb=" C3' DT J 128 " pdb=" O3' DT J 128 " ideal model delta sigma weight residual 1.422 1.470 -0.048 3.00e-02 1.11e+03 2.59e+00 ... (remaining 11181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 15964 2.78 - 5.56: 196 5.56 - 8.35: 7 8.35 - 11.13: 5 11.13 - 13.91: 1 Bond angle restraints: 16173 Sorted by residual: angle pdb=" O3' DC J 135 " pdb=" P DG J 136 " pdb=" O5' DG J 136 " ideal model delta sigma weight residual 104.00 117.91 -13.91 1.50e+00 4.44e-01 8.60e+01 angle pdb=" C3' DC J 135 " pdb=" O3' DC J 135 " pdb=" P DG J 136 " ideal model delta sigma weight residual 120.20 131.11 -10.91 1.50e+00 4.44e-01 5.29e+01 angle pdb=" P DG J 136 " pdb=" O5' DG J 136 " pdb=" C5' DG J 136 " ideal model delta sigma weight residual 120.00 125.98 -5.98 1.50e+00 4.44e-01 1.59e+01 angle pdb=" C3' DC I 111 " pdb=" C2' DC I 111 " pdb=" C1' DC I 111 " ideal model delta sigma weight residual 101.60 96.35 5.25 1.50e+00 4.44e-01 1.23e+01 angle pdb=" C5' DG J 136 " pdb=" C4' DG J 136 " pdb=" O4' DG J 136 " ideal model delta sigma weight residual 109.40 114.50 -5.10 1.50e+00 4.44e-01 1.16e+01 ... (remaining 16168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 4628 34.98 - 69.96: 1358 69.96 - 104.94: 65 104.94 - 139.92: 7 139.92 - 174.90: 2 Dihedral angle restraints: 6060 sinusoidal: 4090 harmonic: 1970 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LYS D 34 " pdb=" C LYS D 34 " pdb=" N GLU D 35 " pdb=" CA GLU D 35 " ideal model delta harmonic sigma weight residual -180.00 -157.78 -22.22 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 6057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1609 0.069 - 0.138: 218 0.138 - 0.207: 19 0.207 - 0.276: 3 0.276 - 0.345: 1 Chirality restraints: 1850 Sorted by residual: chirality pdb=" C1' DT J 13 " pdb=" O4' DT J 13 " pdb=" C2' DT J 13 " pdb=" N1 DT J 13 " both_signs ideal model delta sigma weight residual False 2.47 2.12 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C1' DG I 19 " pdb=" O4' DG I 19 " pdb=" C2' DG I 19 " pdb=" N9 DG I 19 " both_signs ideal model delta sigma weight residual False 2.42 2.17 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" P DG J 136 " pdb=" OP1 DG J 136 " pdb=" OP2 DG J 136 " pdb=" O5' DG J 136 " both_signs ideal model delta sigma weight residual True 2.35 -2.59 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1847 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 13 " -0.036 2.00e-02 2.50e+03 2.52e-02 1.91e+01 pdb=" N9 DG I 13 " 0.069 2.00e-02 2.50e+03 pdb=" C8 DG I 13 " -0.030 2.00e-02 2.50e+03 pdb=" N7 DG I 13 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 13 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 13 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 13 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DG I 13 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 13 " 0.016 2.00e-02 2.50e+03 pdb=" N2 DG I 13 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DG I 13 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DG I 13 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 14 " 0.026 2.00e-02 2.50e+03 2.54e-02 1.78e+01 pdb=" N9 DA J 14 " -0.068 2.00e-02 2.50e+03 pdb=" C8 DA J 14 " 0.040 2.00e-02 2.50e+03 pdb=" N7 DA J 14 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA J 14 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DA J 14 " -0.000 2.00e-02 2.50e+03 pdb=" N6 DA J 14 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DA J 14 " 0.015 2.00e-02 2.50e+03 pdb=" C2 DA J 14 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA J 14 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DA J 14 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 72 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ALA C 72 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA C 72 " -0.022 2.00e-02 2.50e+03 pdb=" N SER C 73 " -0.020 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 352 2.64 - 3.20: 10613 3.20 - 3.77: 22149 3.77 - 4.33: 26096 4.33 - 4.90: 35636 Nonbonded interactions: 94846 Sorted by model distance: nonbonded pdb=" NH2 ARG B 35 " pdb=" OP2 DC I 82 " model vdw 2.074 3.120 nonbonded pdb=" OG SER C 73 " pdb=" O VAL C 78 " model vdw 2.085 3.040 nonbonded pdb=" OG SER G 73 " pdb=" O VAL G 78 " model vdw 2.087 3.040 nonbonded pdb=" N2 DG I 132 " pdb=" O2 DC J 16 " model vdw 2.099 2.496 nonbonded pdb=" O HIS F 75 " pdb=" NH1 ARG H 92 " model vdw 2.154 3.120 ... (remaining 94841 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.760 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 30.720 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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 : 0.007 0.051 11186 Z= 0.384 Angle : 0.836 13.910 16173 Z= 0.502 Chirality : 0.048 0.345 1850 Planarity : 0.005 0.068 1178 Dihedral : 31.368 174.897 4788 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 25.84 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.61 % Favored : 92.79 % Rotamer: Outliers : 0.71 % Allowed : 12.06 % Favored : 87.23 % 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: -2.81 (0.26), residues: 666 helix: -1.35 (0.20), residues: 490 sheet: None (None), residues: 0 loop : -2.95 (0.34), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 113 PHE 0.015 0.003 PHE F 100 TYR 0.015 0.002 TYR D 40 ARG 0.004 0.001 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 0.810 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: A 63 ARG cc_start: 0.7993 (mmp-170) cc_final: 0.7259 (mmp80) REVERT: A 84 PHE cc_start: 0.8620 (m-80) cc_final: 0.8362 (m-80) REVERT: A 90 MET cc_start: 0.8269 (mtp) cc_final: 0.7949 (mtp) REVERT: A 93 GLN cc_start: 0.9115 (tt0) cc_final: 0.8566 (tt0) REVERT: A 97 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8698 (mt-10) REVERT: A 123 ASP cc_start: 0.8910 (m-30) cc_final: 0.8613 (m-30) REVERT: B 27 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8814 (tm-30) REVERT: B 63 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7692 (mt-10) REVERT: B 88 TYR cc_start: 0.8335 (m-10) cc_final: 0.8043 (m-80) REVERT: D 46 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8174 (pttt) REVERT: D 59 MET cc_start: 0.8768 (tpp) cc_final: 0.8280 (tpt) REVERT: D 83 TYR cc_start: 0.7935 (m-10) cc_final: 0.7478 (m-10) REVERT: D 105 GLU cc_start: 0.8753 (pp20) cc_final: 0.7935 (pm20) REVERT: D 106 LEU cc_start: 0.8870 (mt) cc_final: 0.8608 (mt) REVERT: E 60 LEU cc_start: 0.8172 (mt) cc_final: 0.7943 (mt) REVERT: E 97 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8687 (mt-10) REVERT: E 100 LEU cc_start: 0.9430 (tp) cc_final: 0.9150 (tt) REVERT: F 88 TYR cc_start: 0.8285 (m-10) cc_final: 0.7234 (m-80) REVERT: G 36 LEU cc_start: 0.9529 (tt) cc_final: 0.9310 (mm) REVERT: G 46 VAL cc_start: 0.8463 (t) cc_final: 0.8236 (t) REVERT: H 59 MET cc_start: 0.8789 (tpp) cc_final: 0.8525 (tpp) REVERT: H 105 GLU cc_start: 0.8773 (pp20) cc_final: 0.8550 (pp20) outliers start: 4 outliers final: 3 residues processed: 218 average time/residue: 0.3253 time to fit residues: 90.0017 Evaluate side-chains 144 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11186 Z= 0.217 Angle : 0.706 8.339 16173 Z= 0.412 Chirality : 0.041 0.230 1850 Planarity : 0.005 0.064 1178 Dihedral : 34.558 173.269 3476 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.25 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: -0.13 (0.31), residues: 666 helix: 0.84 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -3.11 (0.34), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 82 PHE 0.013 0.002 PHE E 67 TYR 0.013 0.002 TYR F 98 ARG 0.005 0.001 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.805 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 62 ILE cc_start: 0.9180 (mm) cc_final: 0.8941 (mm) REVERT: A 63 ARG cc_start: 0.8274 (mmp-170) cc_final: 0.7673 (mmp80) REVERT: A 84 PHE cc_start: 0.8710 (m-80) cc_final: 0.8223 (m-80) REVERT: A 93 GLN cc_start: 0.8849 (tt0) cc_final: 0.8442 (tt0) REVERT: A 97 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8580 (mt-10) REVERT: A 126 LEU cc_start: 0.9476 (tp) cc_final: 0.9196 (tp) REVERT: B 27 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8733 (tm-30) REVERT: C 31 ARG cc_start: 0.8372 (ttm170) cc_final: 0.7760 (ttp80) REVERT: C 46 VAL cc_start: 0.9050 (t) cc_final: 0.8845 (t) REVERT: D 83 TYR cc_start: 0.7890 (m-10) cc_final: 0.7506 (m-80) REVERT: D 109 HIS cc_start: 0.8717 (m170) cc_final: 0.8494 (m90) REVERT: E 93 GLN cc_start: 0.9058 (tt0) cc_final: 0.8517 (tp40) REVERT: E 97 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8203 (mt-10) REVERT: E 100 LEU cc_start: 0.9257 (tp) cc_final: 0.8963 (tp) REVERT: F 63 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7833 (mt-10) REVERT: H 79 ARG cc_start: 0.8241 (mtp180) cc_final: 0.7898 (mtp85) REVERT: H 83 TYR cc_start: 0.7505 (m-10) cc_final: 0.7030 (m-80) REVERT: H 95 GLN cc_start: 0.9146 (tt0) cc_final: 0.8859 (tt0) REVERT: H 102 LEU cc_start: 0.8676 (tp) cc_final: 0.8420 (tp) REVERT: H 109 HIS cc_start: 0.8971 (m170) cc_final: 0.8606 (m170) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2744 time to fit residues: 73.8136 Evaluate side-chains 163 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 55 optimal weight: 0.4980 chunk 22 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS E 113 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS G 43 HIS H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 11186 Z= 0.366 Angle : 0.762 10.661 16173 Z= 0.441 Chirality : 0.042 0.194 1850 Planarity : 0.006 0.058 1178 Dihedral : 34.525 172.238 3476 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.85 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % 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: 0.15 (0.31), residues: 666 helix: 1.06 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -3.11 (0.34), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 75 PHE 0.017 0.003 PHE B 100 TYR 0.017 0.003 TYR B 88 ARG 0.006 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.9255 (mm) cc_final: 0.8904 (mm) REVERT: A 63 ARG cc_start: 0.8361 (mmp-170) cc_final: 0.7676 (mmp80) REVERT: A 70 LEU cc_start: 0.9614 (pp) cc_final: 0.9230 (tt) REVERT: A 72 ARG cc_start: 0.8934 (mpt180) cc_final: 0.8462 (mpt180) REVERT: A 93 GLN cc_start: 0.8919 (tt0) cc_final: 0.8571 (tt0) REVERT: A 126 LEU cc_start: 0.9587 (tp) cc_final: 0.9334 (tp) REVERT: A 128 ARG cc_start: 0.9047 (mtp-110) cc_final: 0.8804 (mmm-85) REVERT: B 27 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8623 (tm-30) REVERT: C 31 ARG cc_start: 0.8344 (ttm170) cc_final: 0.7988 (ttp80) REVERT: C 45 ARG cc_start: 0.8179 (mtp-110) cc_final: 0.7850 (mtp-110) REVERT: C 57 ILE cc_start: 0.9162 (mm) cc_final: 0.8952 (mm) REVERT: D 42 TYR cc_start: 0.8927 (m-80) cc_final: 0.8627 (m-80) REVERT: D 80 LEU cc_start: 0.9642 (mt) cc_final: 0.9278 (mt) REVERT: D 83 TYR cc_start: 0.7750 (m-10) cc_final: 0.7485 (m-80) REVERT: G 34 ARG cc_start: 0.8525 (mtm110) cc_final: 0.7886 (mtm180) REVERT: G 59 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8823 (mm-30) REVERT: H 80 LEU cc_start: 0.9561 (mt) cc_final: 0.9244 (mt) REVERT: H 83 TYR cc_start: 0.7690 (m-10) cc_final: 0.7403 (m-80) REVERT: H 105 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8326 (tm-30) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2641 time to fit residues: 61.0940 Evaluate side-chains 129 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11186 Z= 0.244 Angle : 0.687 7.940 16173 Z= 0.401 Chirality : 0.040 0.237 1850 Planarity : 0.005 0.060 1178 Dihedral : 34.309 173.519 3476 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.40 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: 0.52 (0.31), residues: 666 helix: 1.34 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -2.97 (0.36), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.013 0.002 PHE D 70 TYR 0.029 0.002 TYR D 40 ARG 0.006 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.9220 (mm) cc_final: 0.8947 (mm) REVERT: A 63 ARG cc_start: 0.8487 (mmp-170) cc_final: 0.7860 (mmp80) REVERT: A 70 LEU cc_start: 0.9606 (pp) cc_final: 0.9254 (tt) REVERT: A 93 GLN cc_start: 0.8965 (tt0) cc_final: 0.8513 (tt0) REVERT: A 126 LEU cc_start: 0.9618 (tp) cc_final: 0.9403 (tp) REVERT: B 63 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7875 (mt-10) REVERT: C 31 ARG cc_start: 0.8357 (ttm170) cc_final: 0.8149 (ttp80) REVERT: C 45 ARG cc_start: 0.8005 (mtp-110) cc_final: 0.7758 (mtp-110) REVERT: C 66 LEU cc_start: 0.8938 (mt) cc_final: 0.8541 (pp) REVERT: D 42 TYR cc_start: 0.8765 (m-80) cc_final: 0.8518 (m-80) REVERT: D 102 LEU cc_start: 0.8254 (tp) cc_final: 0.7959 (tp) REVERT: D 109 HIS cc_start: 0.8481 (m90) cc_final: 0.8053 (m170) REVERT: E 94 GLU cc_start: 0.8672 (tt0) cc_final: 0.8350 (tt0) REVERT: G 59 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8757 (mm-30) REVERT: G 66 LEU cc_start: 0.8934 (mt) cc_final: 0.8658 (pp) REVERT: H 42 TYR cc_start: 0.9015 (m-80) cc_final: 0.8675 (m-80) REVERT: H 80 LEU cc_start: 0.9534 (mt) cc_final: 0.9166 (mt) REVERT: H 102 LEU cc_start: 0.8546 (tp) cc_final: 0.8255 (tp) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2655 time to fit residues: 64.0850 Evaluate side-chains 144 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 17 optimal weight: 0.0370 overall best weight: 3.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN E 93 GLN G 21 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11186 Z= 0.313 Angle : 0.719 8.007 16173 Z= 0.417 Chirality : 0.041 0.215 1850 Planarity : 0.006 0.058 1178 Dihedral : 34.323 172.373 3476 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.60 % Allowed : 1.80 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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: 0.40 (0.31), residues: 666 helix: 1.23 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -2.91 (0.36), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.019 0.002 PHE E 104 TYR 0.026 0.002 TYR H 83 ARG 0.007 0.001 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.809 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 62 ILE cc_start: 0.9265 (mm) cc_final: 0.8943 (mm) REVERT: A 63 ARG cc_start: 0.8492 (mmp-170) cc_final: 0.7930 (mmp80) REVERT: A 70 LEU cc_start: 0.9646 (pp) cc_final: 0.9270 (tt) REVERT: A 93 GLN cc_start: 0.8950 (tt0) cc_final: 0.8559 (tt0) REVERT: A 126 LEU cc_start: 0.9665 (tp) cc_final: 0.9413 (tp) REVERT: B 63 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7910 (mt-10) REVERT: C 46 VAL cc_start: 0.8984 (t) cc_final: 0.8777 (t) REVERT: G 59 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8818 (mm-30) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2486 time to fit residues: 55.3219 Evaluate side-chains 119 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11186 Z= 0.213 Angle : 0.673 7.889 16173 Z= 0.390 Chirality : 0.039 0.246 1850 Planarity : 0.005 0.061 1178 Dihedral : 34.160 173.022 3476 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.40 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: 0.67 (0.32), residues: 666 helix: 1.41 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -2.74 (0.38), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 113 PHE 0.014 0.002 PHE D 70 TYR 0.027 0.002 TYR H 83 ARG 0.006 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8496 (mmp-170) cc_final: 0.7992 (mmp80) REVERT: A 70 LEU cc_start: 0.9624 (pp) cc_final: 0.9287 (tt) REVERT: A 93 GLN cc_start: 0.8914 (tt0) cc_final: 0.8609 (tt0) REVERT: A 126 LEU cc_start: 0.9637 (tp) cc_final: 0.9384 (tp) REVERT: B 53 GLU cc_start: 0.7933 (mp0) cc_final: 0.7673 (mp0) REVERT: B 63 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 66 LEU cc_start: 0.8965 (mt) cc_final: 0.8550 (pp) REVERT: D 80 LEU cc_start: 0.9472 (mt) cc_final: 0.9021 (mp) REVERT: D 102 LEU cc_start: 0.8328 (tp) cc_final: 0.8035 (tp) REVERT: F 49 LEU cc_start: 0.8998 (mp) cc_final: 0.8590 (mp) REVERT: F 63 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7987 (mt-10) REVERT: G 57 ILE cc_start: 0.9221 (mm) cc_final: 0.9007 (mm) REVERT: G 59 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8706 (mm-30) REVERT: G 66 LEU cc_start: 0.8928 (mt) cc_final: 0.8651 (pp) REVERT: H 102 LEU cc_start: 0.8468 (tp) cc_final: 0.8252 (tp) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2267 time to fit residues: 55.4358 Evaluate side-chains 120 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11186 Z= 0.218 Angle : 0.675 8.868 16173 Z= 0.387 Chirality : 0.039 0.271 1850 Planarity : 0.005 0.059 1178 Dihedral : 34.102 171.641 3476 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.10 % Favored : 97.30 % Rotamer: Outliers : 0.18 % Allowed : 1.60 % Favored : 98.23 % 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: 0.65 (0.31), residues: 666 helix: 1.35 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -2.72 (0.38), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 35 PHE 0.014 0.002 PHE A 104 TYR 0.028 0.002 TYR D 83 ARG 0.006 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8421 (mmp-170) cc_final: 0.7928 (mmp80) REVERT: A 70 LEU cc_start: 0.9626 (pp) cc_final: 0.9280 (tt) REVERT: A 93 GLN cc_start: 0.8880 (tt0) cc_final: 0.8518 (tt0) REVERT: A 126 LEU cc_start: 0.9590 (tp) cc_final: 0.9353 (tp) REVERT: B 63 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 31 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.7912 (ttp-170) REVERT: C 66 LEU cc_start: 0.8940 (mt) cc_final: 0.8557 (pp) REVERT: D 83 TYR cc_start: 0.7919 (m-80) cc_final: 0.7142 (m-80) REVERT: D 102 LEU cc_start: 0.8358 (tp) cc_final: 0.8114 (tp) REVERT: E 128 ARG cc_start: 0.9439 (mmm-85) cc_final: 0.9156 (mmm-85) REVERT: F 58 LEU cc_start: 0.9381 (mm) cc_final: 0.8976 (pp) REVERT: F 62 LEU cc_start: 0.9722 (mm) cc_final: 0.9519 (mm) REVERT: G 59 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8725 (mm-30) REVERT: G 66 LEU cc_start: 0.8851 (mt) cc_final: 0.8591 (pp) REVERT: H 99 ARG cc_start: 0.9219 (ttm170) cc_final: 0.9009 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.2303 time to fit residues: 57.2321 Evaluate side-chains 131 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11186 Z= 0.260 Angle : 0.683 8.072 16173 Z= 0.395 Chirality : 0.040 0.251 1850 Planarity : 0.005 0.060 1178 Dihedral : 34.165 171.288 3476 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.55 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 0.65 (0.32), residues: 666 helix: 1.33 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -2.60 (0.40), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 113 PHE 0.019 0.002 PHE E 104 TYR 0.024 0.002 TYR D 83 ARG 0.005 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.9168 (mm) cc_final: 0.8933 (mm) REVERT: A 63 ARG cc_start: 0.8452 (mmp-170) cc_final: 0.7883 (mmp80) REVERT: A 70 LEU cc_start: 0.9635 (pp) cc_final: 0.9268 (tt) REVERT: A 93 GLN cc_start: 0.8915 (tt0) cc_final: 0.8541 (tt0) REVERT: C 66 LEU cc_start: 0.8968 (mt) cc_final: 0.8580 (pp) REVERT: D 80 LEU cc_start: 0.9422 (mt) cc_final: 0.9033 (mp) REVERT: D 83 TYR cc_start: 0.7564 (m-80) cc_final: 0.7348 (m-80) REVERT: E 76 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8544 (tm-30) REVERT: G 59 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8637 (mm-30) REVERT: G 66 LEU cc_start: 0.8915 (mt) cc_final: 0.8626 (pp) REVERT: G 91 ARG cc_start: 0.8558 (mmt180) cc_final: 0.7979 (mmt180) REVERT: H 99 ARG cc_start: 0.9254 (ttm170) cc_final: 0.9042 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2312 time to fit residues: 53.4583 Evaluate side-chains 125 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11186 Z= 0.319 Angle : 0.719 8.198 16173 Z= 0.417 Chirality : 0.041 0.243 1850 Planarity : 0.006 0.060 1178 Dihedral : 34.260 171.734 3476 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.70 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: 0.38 (0.31), residues: 666 helix: 1.13 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -2.68 (0.39), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 113 PHE 0.016 0.002 PHE E 104 TYR 0.022 0.002 TYR F 72 ARG 0.005 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.9196 (mm) cc_final: 0.8790 (mm) REVERT: A 63 ARG cc_start: 0.8446 (mmp-170) cc_final: 0.7938 (mmp80) REVERT: A 70 LEU cc_start: 0.9631 (pp) cc_final: 0.9268 (tt) REVERT: A 93 GLN cc_start: 0.8950 (tt0) cc_final: 0.8558 (tt0) REVERT: B 88 TYR cc_start: 0.8268 (m-80) cc_final: 0.7596 (m-80) REVERT: C 66 LEU cc_start: 0.8989 (mt) cc_final: 0.8581 (pp) REVERT: D 83 TYR cc_start: 0.7946 (m-80) cc_final: 0.7343 (m-80) REVERT: E 90 MET cc_start: 0.8428 (mtt) cc_final: 0.8210 (mtt) REVERT: F 53 GLU cc_start: 0.8349 (mp0) cc_final: 0.8049 (mp0) REVERT: G 59 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8719 (mm-30) REVERT: G 66 LEU cc_start: 0.8967 (mt) cc_final: 0.8693 (pp) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2367 time to fit residues: 53.2520 Evaluate side-chains 117 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.0870 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11186 Z= 0.204 Angle : 0.671 8.715 16173 Z= 0.386 Chirality : 0.039 0.259 1850 Planarity : 0.005 0.065 1178 Dihedral : 34.034 172.647 3476 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.60 % Allowed : 1.95 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.58 (0.32), residues: 666 helix: 1.27 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -2.67 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.019 0.002 PHE E 84 TYR 0.025 0.002 TYR B 88 ARG 0.007 0.001 ARG A 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.9206 (mm) cc_final: 0.8971 (mm) REVERT: A 63 ARG cc_start: 0.8441 (mmp-170) cc_final: 0.7894 (mmp80) REVERT: A 70 LEU cc_start: 0.9631 (pp) cc_final: 0.9276 (tt) REVERT: A 93 GLN cc_start: 0.8881 (tt0) cc_final: 0.8528 (tt0) REVERT: A 126 LEU cc_start: 0.9587 (tp) cc_final: 0.9383 (tp) REVERT: B 53 GLU cc_start: 0.7740 (mp0) cc_final: 0.7536 (mp0) REVERT: B 63 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7835 (mt-10) REVERT: B 88 TYR cc_start: 0.8121 (m-80) cc_final: 0.7606 (m-80) REVERT: C 66 LEU cc_start: 0.8996 (mt) cc_final: 0.8570 (pp) REVERT: D 80 LEU cc_start: 0.9603 (mt) cc_final: 0.9356 (mt) REVERT: D 83 TYR cc_start: 0.7820 (m-80) cc_final: 0.7347 (m-80) REVERT: E 84 PHE cc_start: 0.8859 (m-80) cc_final: 0.8469 (m-80) REVERT: E 90 MET cc_start: 0.8151 (mtt) cc_final: 0.7926 (mtt) REVERT: G 66 LEU cc_start: 0.8872 (mt) cc_final: 0.8578 (pp) REVERT: H 102 LEU cc_start: 0.8650 (tp) cc_final: 0.8387 (tp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2330 time to fit residues: 55.2800 Evaluate side-chains 131 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** 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 = 0.3328 r_free = 0.3328 target = 0.048780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.037182 restraints weight = 85564.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.038291 restraints weight = 50110.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.039071 restraints weight = 35255.825| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.6503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11186 Z= 0.206 Angle : 0.681 8.686 16173 Z= 0.391 Chirality : 0.039 0.211 1850 Planarity : 0.005 0.064 1178 Dihedral : 34.027 172.334 3476 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.55 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.53 (0.32), residues: 666 helix: 1.23 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -2.65 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 35 PHE 0.016 0.002 PHE E 84 TYR 0.025 0.002 TYR B 88 ARG 0.007 0.001 ARG H 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1865.83 seconds wall clock time: 34 minutes 21.30 seconds (2061.30 seconds total)