Starting phenix.real_space_refine on Wed Feb 14 22:45:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/02_2024/6m4d_30076.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/02_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_30076/02_2024/6m4d_30076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/02_2024/6m4d_30076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/02_2024/6m4d_30076.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/02_2024/6m4d_30076.pdb" } 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 Residue "A GLU 94": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 94": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10497 Number of models: 1 Model: "" Number of chains: 10 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: "E" 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: "F" 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: "G" 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: "H" 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} Time building chain proxies: 5.88, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.97 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: 3.31 Time building geometry restraints manager: 7.05 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: 96.35 - 103.62: 636 103.62 - 110.90: 5407 110.90 - 118.17: 3772 118.17 - 125.44: 5541 125.44 - 132.72: 817 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 2.520 nonbonded pdb=" OG SER C 73 " pdb=" O VAL C 78 " model vdw 2.085 2.440 nonbonded pdb=" OG SER G 73 " pdb=" O VAL G 78 " model vdw 2.087 2.440 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 2.520 ... (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 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.910 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 36.300 Find NCS groups from input model: 0.500 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.850 ------------------------------------------------------------------------------- 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 : 0.858 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: 0.3284 time to fit residues: 91.1786 Evaluate side-chains 144 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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: 0.7980 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 HIS G 43 HIS H 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11186 Z= 0.223 Angle : 0.703 9.293 16173 Z= 0.410 Chirality : 0.040 0.248 1850 Planarity : 0.005 0.065 1178 Dihedral : 34.554 172.864 3476 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.85 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: -0.23 (0.30), residues: 666 helix: 0.73 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -2.99 (0.34), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.011 0.002 PHE A 104 TYR 0.012 0.001 TYR F 98 ARG 0.005 0.001 ARG A 131 *********************** 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 200 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8356 (mmp-170) cc_final: 0.7794 (mmp80) REVERT: A 84 PHE cc_start: 0.8743 (m-80) cc_final: 0.8308 (m-80) REVERT: A 93 GLN cc_start: 0.8818 (tt0) cc_final: 0.8371 (tt0) REVERT: A 97 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8604 (mt-10) REVERT: A 126 LEU cc_start: 0.9489 (tp) cc_final: 0.9220 (tp) REVERT: B 27 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8784 (tm-30) REVERT: B 63 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7767 (mt-10) REVERT: B 88 TYR cc_start: 0.8019 (m-10) cc_final: 0.7493 (m-80) REVERT: C 31 ARG cc_start: 0.8267 (ttm170) cc_final: 0.7834 (ttp80) REVERT: C 45 ARG cc_start: 0.8113 (mtp-110) cc_final: 0.7645 (mtp-110) REVERT: C 46 VAL cc_start: 0.9065 (t) cc_final: 0.8789 (t) REVERT: D 59 MET cc_start: 0.8771 (tpp) cc_final: 0.8542 (mmm) REVERT: D 109 HIS cc_start: 0.8708 (m170) cc_final: 0.8364 (m170) REVERT: E 100 LEU cc_start: 0.9296 (tp) cc_final: 0.9008 (tp) REVERT: F 63 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7868 (mt-10) REVERT: G 31 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7660 (ttp80) REVERT: G 46 VAL cc_start: 0.8485 (t) cc_final: 0.8272 (t) REVERT: H 79 ARG cc_start: 0.8416 (mtp180) cc_final: 0.7908 (mtp85) REVERT: H 83 TYR cc_start: 0.7420 (m-10) cc_final: 0.6790 (m-80) REVERT: H 95 GLN cc_start: 0.9122 (tt0) cc_final: 0.8867 (tt0) REVERT: H 102 LEU cc_start: 0.8571 (tp) cc_final: 0.8341 (tp) REVERT: H 109 HIS cc_start: 0.8943 (m170) cc_final: 0.8600 (m170) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2693 time to fit residues: 71.1356 Evaluate side-chains 159 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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: 0.9980 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3705 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= 0.229 Angle : 0.667 8.292 16173 Z= 0.389 Chirality : 0.039 0.271 1850 Planarity : 0.005 0.062 1178 Dihedral : 34.294 173.419 3476 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.25 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % 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: 0.68 (0.32), residues: 666 helix: 1.45 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -2.92 (0.35), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.002 HIS H 109 PHE 0.012 0.002 PHE E 67 TYR 0.036 0.002 TYR H 40 ARG 0.007 0.001 ARG F 39 *********************** 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 194 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 0.948 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: A 63 ARG cc_start: 0.8411 (mmp-170) cc_final: 0.7824 (mmp80) REVERT: A 70 LEU cc_start: 0.9642 (pp) cc_final: 0.9216 (tt) REVERT: A 84 PHE cc_start: 0.8826 (m-80) cc_final: 0.8401 (m-80) REVERT: A 93 GLN cc_start: 0.8765 (tt0) cc_final: 0.8387 (tt0) REVERT: A 126 LEU cc_start: 0.9576 (tp) cc_final: 0.9323 (tp) REVERT: B 27 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8668 (tm-30) REVERT: B 63 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7929 (mt-10) REVERT: D 83 TYR cc_start: 0.7699 (m-10) cc_final: 0.7087 (m-80) REVERT: D 102 LEU cc_start: 0.8284 (tp) cc_final: 0.8036 (tp) REVERT: F 88 TYR cc_start: 0.8090 (m-80) cc_final: 0.7613 (m-80) REVERT: G 34 ARG cc_start: 0.9069 (mtp180) cc_final: 0.7953 (mtm180) REVERT: G 46 VAL cc_start: 0.8634 (t) cc_final: 0.8393 (t) REVERT: H 79 ARG cc_start: 0.8351 (mtp180) cc_final: 0.7726 (mtp85) REVERT: H 80 LEU cc_start: 0.9558 (mt) cc_final: 0.9292 (mt) REVERT: H 83 TYR cc_start: 0.7368 (m-10) cc_final: 0.6914 (m-80) REVERT: H 105 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8273 (tm-30) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2841 time to fit residues: 72.8347 Evaluate side-chains 142 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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: 7.9990 chunk 42 optimal weight: 8.9990 chunk 9 optimal weight: 0.0570 chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 0.1980 chunk 82 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.8502 ------------------------------------------------------------------------------- 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 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** F 27 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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= 0.227 Angle : 0.670 7.408 16173 Z= 0.389 Chirality : 0.039 0.269 1850 Planarity : 0.005 0.059 1178 Dihedral : 34.168 172.778 3476 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.55 % Favored : 96.85 % Rotamer: Outliers : 0.18 % Allowed : 3.72 % Favored : 96.10 % 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: 0.82 (0.32), residues: 666 helix: 1.55 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -2.89 (0.36), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 35 PHE 0.012 0.002 PHE H 70 TYR 0.032 0.002 TYR H 40 ARG 0.007 0.001 ARG G 31 *********************** 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 194 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 0.913 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: 0.9235 (mm) cc_final: 0.9030 (mm) REVERT: A 63 ARG cc_start: 0.8470 (mmp-170) cc_final: 0.7817 (mmp80) REVERT: A 70 LEU cc_start: 0.9614 (pp) cc_final: 0.9214 (tt) REVERT: A 84 PHE cc_start: 0.8837 (m-80) cc_final: 0.8363 (m-80) REVERT: A 93 GLN cc_start: 0.8735 (tt0) cc_final: 0.8261 (tt0) REVERT: A 97 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8565 (mt-10) REVERT: B 63 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7856 (mt-10) REVERT: C 31 ARG cc_start: 0.8326 (ttm170) cc_final: 0.7834 (ttp80) REVERT: D 83 TYR cc_start: 0.7699 (m-10) cc_final: 0.7458 (m-80) REVERT: D 102 LEU cc_start: 0.8257 (tp) cc_final: 0.8009 (tp) REVERT: D 106 LEU cc_start: 0.9133 (mt) cc_final: 0.8330 (mt) REVERT: F 63 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7870 (mt-10) REVERT: F 84 MET cc_start: 0.7937 (tpt) cc_final: 0.7604 (tpp) REVERT: G 31 ARG cc_start: 0.8785 (mmp-170) cc_final: 0.8180 (mmm160) REVERT: G 34 ARG cc_start: 0.8909 (mtp180) cc_final: 0.8416 (mtp180) REVERT: G 46 VAL cc_start: 0.8699 (t) cc_final: 0.8472 (t) REVERT: H 42 TYR cc_start: 0.9004 (m-80) cc_final: 0.8607 (m-80) REVERT: H 79 ARG cc_start: 0.8411 (mtp180) cc_final: 0.7748 (mtp85) REVERT: H 80 LEU cc_start: 0.9569 (mt) cc_final: 0.9201 (mt) REVERT: H 83 TYR cc_start: 0.7598 (m-10) cc_final: 0.7245 (m-80) REVERT: H 102 LEU cc_start: 0.8632 (tp) cc_final: 0.8338 (tp) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.2655 time to fit residues: 68.1355 Evaluate side-chains 138 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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: 0.9980 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 17 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11186 Z= 0.186 Angle : 0.641 8.010 16173 Z= 0.371 Chirality : 0.038 0.292 1850 Planarity : 0.005 0.061 1178 Dihedral : 34.003 172.376 3476 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.40 % Favored : 97.00 % Rotamer: Outliers : 0.18 % Allowed : 2.48 % Favored : 97.34 % 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: 0.96 (0.32), residues: 666 helix: 1.63 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -2.72 (0.40), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 113 PHE 0.013 0.001 PHE E 104 TYR 0.025 0.002 TYR F 88 ARG 0.005 0.000 ARG E 128 *********************** 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 199 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 0.744 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 63 ARG cc_start: 0.8404 (mmp-170) cc_final: 0.7963 (mmp80) REVERT: A 70 LEU cc_start: 0.9591 (pp) cc_final: 0.9219 (tt) REVERT: A 84 PHE cc_start: 0.8773 (m-80) cc_final: 0.8303 (m-80) REVERT: A 93 GLN cc_start: 0.8693 (tt0) cc_final: 0.8359 (tt0) REVERT: A 126 LEU cc_start: 0.9498 (tp) cc_final: 0.9192 (tp) REVERT: B 53 GLU cc_start: 0.7855 (mp0) cc_final: 0.7507 (mp0) REVERT: B 63 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7819 (mt-10) REVERT: B 75 HIS cc_start: 0.9270 (t70) cc_final: 0.8957 (t70) REVERT: C 45 ARG cc_start: 0.7893 (mtp-110) cc_final: 0.7635 (mtp-110) REVERT: D 80 LEU cc_start: 0.9605 (mt) cc_final: 0.9348 (mt) REVERT: D 83 TYR cc_start: 0.7766 (m-10) cc_final: 0.7486 (m-80) REVERT: D 102 LEU cc_start: 0.8277 (tp) cc_final: 0.8010 (tp) REVERT: D 109 HIS cc_start: 0.8865 (m170) cc_final: 0.8278 (m170) REVERT: F 75 HIS cc_start: 0.9244 (t70) cc_final: 0.8877 (t70) REVERT: G 34 ARG cc_start: 0.8777 (mtp180) cc_final: 0.8280 (mmm-85) REVERT: H 42 TYR cc_start: 0.8879 (m-80) cc_final: 0.8610 (m-80) REVERT: H 79 ARG cc_start: 0.8458 (mtp180) cc_final: 0.8256 (mtp180) REVERT: H 102 LEU cc_start: 0.8420 (tp) cc_final: 0.8144 (tp) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.2657 time to fit residues: 70.2909 Evaluate side-chains 136 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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: 5.9990 chunk 21 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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** A 113 HIS ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11186 Z= 0.317 Angle : 0.709 7.726 16173 Z= 0.409 Chirality : 0.040 0.265 1850 Planarity : 0.005 0.053 1178 Dihedral : 34.138 171.179 3476 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 23.57 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.30 % Favored : 96.10 % 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: 0.57 (0.31), residues: 666 helix: 1.34 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -2.78 (0.36), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS D 109 PHE 0.015 0.002 PHE H 70 TYR 0.016 0.002 TYR D 40 ARG 0.009 0.001 ARG D 92 *********************** 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 169 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.806 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: 0.9248 (mm) cc_final: 0.8966 (mm) REVERT: A 63 ARG cc_start: 0.8477 (mmp-170) cc_final: 0.7881 (mmp80) REVERT: A 70 LEU cc_start: 0.9656 (pp) cc_final: 0.9229 (tt) REVERT: A 93 GLN cc_start: 0.8682 (tt0) cc_final: 0.8399 (tt0) REVERT: A 128 ARG cc_start: 0.8731 (mtp85) cc_final: 0.8413 (mmm-85) REVERT: B 75 HIS cc_start: 0.9278 (t70) cc_final: 0.8953 (t70) REVERT: C 46 VAL cc_start: 0.9023 (t) cc_final: 0.8811 (t) REVERT: D 102 LEU cc_start: 0.8289 (tp) cc_final: 0.8064 (tp) REVERT: G 31 ARG cc_start: 0.8784 (mmm160) cc_final: 0.7597 (mmm160) REVERT: G 34 ARG cc_start: 0.8591 (mtp180) cc_final: 0.8241 (mtp180) REVERT: H 102 LEU cc_start: 0.8547 (tp) cc_final: 0.8330 (tp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2504 time to fit residues: 57.0155 Evaluate side-chains 125 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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: 0.9990 chunk 49 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 35 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: 0.8108 moved from start: 0.5575 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= 0.208 Angle : 0.651 8.097 16173 Z= 0.376 Chirality : 0.038 0.246 1850 Planarity : 0.005 0.056 1178 Dihedral : 34.027 172.520 3476 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.55 % Favored : 96.85 % Rotamer: Outliers : 0.18 % Allowed : 2.30 % 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: 0.86 (0.32), residues: 666 helix: 1.57 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -2.71 (0.37), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 109 PHE 0.015 0.002 PHE D 70 TYR 0.017 0.001 TYR D 42 ARG 0.007 0.001 ARG H 86 *********************** 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 178 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 0.761 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 63 ARG cc_start: 0.8486 (mmp-170) cc_final: 0.7935 (mmp80) REVERT: A 70 LEU cc_start: 0.9647 (pp) cc_final: 0.9248 (tt) REVERT: A 84 PHE cc_start: 0.8855 (m-80) cc_final: 0.8507 (m-80) REVERT: A 93 GLN cc_start: 0.8710 (tt0) cc_final: 0.8375 (tt0) REVERT: B 53 GLU cc_start: 0.7821 (mp0) cc_final: 0.7424 (mp0) REVERT: B 63 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7875 (mt-10) REVERT: B 75 HIS cc_start: 0.9240 (t70) cc_final: 0.8875 (t70) REVERT: C 46 VAL cc_start: 0.9049 (t) cc_final: 0.8811 (t) REVERT: C 66 LEU cc_start: 0.8885 (mt) cc_final: 0.8522 (pp) REVERT: D 102 LEU cc_start: 0.8271 (tp) cc_final: 0.8006 (tp) REVERT: F 49 LEU cc_start: 0.8893 (mp) cc_final: 0.8548 (mp) REVERT: F 75 HIS cc_start: 0.9235 (t-90) cc_final: 0.8898 (t-90) REVERT: G 31 ARG cc_start: 0.8783 (mmm160) cc_final: 0.7542 (mmm160) REVERT: G 34 ARG cc_start: 0.8584 (mtp180) cc_final: 0.8233 (mtp180) REVERT: G 46 VAL cc_start: 0.8668 (t) cc_final: 0.8442 (t) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.2509 time to fit residues: 60.4864 Evaluate side-chains 125 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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: 8.9990 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5696 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= 0.234 Angle : 0.661 8.079 16173 Z= 0.381 Chirality : 0.038 0.244 1850 Planarity : 0.005 0.057 1178 Dihedral : 34.032 171.564 3476 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.00 % Favored : 96.40 % 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: 0.97 (0.32), residues: 666 helix: 1.63 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -2.60 (0.38), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 82 PHE 0.015 0.002 PHE A 104 TYR 0.030 0.002 TYR H 83 ARG 0.012 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 177 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.775 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: 0.9249 (mm) cc_final: 0.9037 (mm) REVERT: A 63 ARG cc_start: 0.8438 (mmp-170) cc_final: 0.7863 (mmp80) REVERT: A 70 LEU cc_start: 0.9654 (pp) cc_final: 0.9241 (tt) REVERT: A 93 GLN cc_start: 0.8659 (tt0) cc_final: 0.8361 (tt0) REVERT: B 53 GLU cc_start: 0.7732 (mp0) cc_final: 0.7461 (mp0) REVERT: B 63 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7834 (mt-10) REVERT: B 75 HIS cc_start: 0.9296 (t70) cc_final: 0.8938 (t70) REVERT: C 31 ARG cc_start: 0.8140 (ttm170) cc_final: 0.6757 (ttp-170) REVERT: C 66 LEU cc_start: 0.8876 (mt) cc_final: 0.8530 (pp) REVERT: F 63 GLU cc_start: 0.8688 (pt0) cc_final: 0.8349 (pt0) REVERT: G 46 VAL cc_start: 0.8724 (t) cc_final: 0.8517 (t) REVERT: H 83 TYR cc_start: 0.7616 (m-80) cc_final: 0.7228 (m-80) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2571 time to fit residues: 60.8819 Evaluate side-chains 120 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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: 10.0000 chunk 35 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS G 71 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 11186 Z= 0.424 Angle : 0.803 13.116 16173 Z= 0.459 Chirality : 0.043 0.219 1850 Planarity : 0.006 0.055 1178 Dihedral : 34.343 172.188 3476 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 29.38 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.60 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 0.12 (0.30), residues: 666 helix: 0.99 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -2.80 (0.37), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS B 75 PHE 0.026 0.003 PHE E 104 TYR 0.025 0.002 TYR H 83 ARG 0.011 0.001 ARG H 92 *********************** 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 147 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.820 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: 0.9376 (mm) cc_final: 0.8986 (mm) REVERT: A 63 ARG cc_start: 0.8459 (mmp-170) cc_final: 0.7924 (mmp80) REVERT: A 70 LEU cc_start: 0.9649 (pp) cc_final: 0.9242 (tt) REVERT: B 27 GLN cc_start: 0.8309 (mp10) cc_final: 0.8078 (mp10) REVERT: B 52 GLU cc_start: 0.8305 (pm20) cc_final: 0.8008 (pm20) REVERT: B 75 HIS cc_start: 0.9399 (t70) cc_final: 0.9079 (t70) REVERT: C 46 VAL cc_start: 0.8986 (t) cc_final: 0.8779 (t) REVERT: F 63 GLU cc_start: 0.8646 (pt0) cc_final: 0.8305 (pt0) REVERT: F 75 HIS cc_start: 0.9105 (t-90) cc_final: 0.8847 (t70) REVERT: H 83 TYR cc_start: 0.7546 (m-80) cc_final: 0.6962 (m-80) REVERT: H 99 ARG cc_start: 0.9208 (ttm170) cc_final: 0.9002 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2856 time to fit residues: 55.5959 Evaluate side-chains 109 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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: 2.9990 chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 0.0010 chunk 76 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.1792 ------------------------------------------------------------------------------- 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 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.6107 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= 0.210 Angle : 0.697 8.579 16173 Z= 0.397 Chirality : 0.039 0.248 1850 Planarity : 0.005 0.061 1178 Dihedral : 34.140 174.206 3476 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.25 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 0.62 (0.32), residues: 666 helix: 1.36 (0.23), residues: 500 sheet: None (None), residues: 0 loop : -2.60 (0.38), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 33 PHE 0.020 0.002 PHE E 104 TYR 0.035 0.002 TYR H 83 ARG 0.008 0.001 ARG H 92 ********************** 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 : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8500 (mmp-170) cc_final: 0.7978 (mmp80) REVERT: A 70 LEU cc_start: 0.9628 (pp) cc_final: 0.9229 (tt) REVERT: A 93 GLN cc_start: 0.8637 (tp40) cc_final: 0.8399 (tp40) REVERT: B 27 GLN cc_start: 0.8308 (mp10) cc_final: 0.8084 (mp10) REVERT: B 53 GLU cc_start: 0.7934 (mp0) cc_final: 0.7709 (mp0) REVERT: B 63 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7872 (mt-10) REVERT: B 88 TYR cc_start: 0.8282 (m-80) cc_final: 0.8051 (m-80) REVERT: C 31 ARG cc_start: 0.7735 (ttm170) cc_final: 0.7073 (ttp80) REVERT: C 66 LEU cc_start: 0.8912 (mt) cc_final: 0.8538 (pp) REVERT: F 63 GLU cc_start: 0.8608 (pt0) cc_final: 0.8252 (pt0) REVERT: F 75 HIS cc_start: 0.9108 (t-90) cc_final: 0.8707 (t70) REVERT: F 88 TYR cc_start: 0.8074 (m-10) cc_final: 0.7622 (m-10) REVERT: G 57 ILE cc_start: 0.9245 (mm) cc_final: 0.9002 (mm) REVERT: H 35 GLU cc_start: 0.7271 (tp30) cc_final: 0.6820 (tp30) REVERT: H 80 LEU cc_start: 0.9559 (mt) cc_final: 0.9320 (mm) REVERT: H 83 TYR cc_start: 0.7778 (m-80) cc_final: 0.7058 (m-80) REVERT: H 99 ARG cc_start: 0.9139 (ttm170) cc_final: 0.8864 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2728 time to fit residues: 63.8448 Evaluate side-chains 129 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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: 3.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.050094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.038638 restraints weight = 85341.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.039809 restraints weight = 49440.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.040615 restraints weight = 34547.972| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.6521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11186 Z= 0.195 Angle : 0.671 8.641 16173 Z= 0.383 Chirality : 0.039 0.261 1850 Planarity : 0.005 0.061 1178 Dihedral : 33.855 172.675 3476 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.25 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 0.68 (0.32), residues: 666 helix: 1.34 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -2.41 (0.39), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.001 HIS G 35 PHE 0.014 0.001 PHE E 104 TYR 0.031 0.002 TYR H 40 ARG 0.008 0.001 ARG H 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1941.35 seconds wall clock time: 36 minutes 11.35 seconds (2171.35 seconds total)