Starting phenix.real_space_refine on Sat Mar 16 16:21:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pff_13374/03_2024/7pff_13374.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pff_13374/03_2024/7pff_13374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pff_13374/03_2024/7pff_13374.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pff_13374/03_2024/7pff_13374.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pff_13374/03_2024/7pff_13374.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pff_13374/03_2024/7pff_13374.pdb" } resolution = 4.3 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. 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 334 5.49 5 S 10 5.16 5 C 7085 2.51 5 N 2430 2.21 5 O 3076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 52": "OE1" <-> "OE2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "N PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 41": "OE1" <-> "OE2" Residue "Q GLU 64": "OE1" <-> "OE2" Residue "R PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 113": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12935 Number of models: 1 Model: "" Number of chains: 10 Chain: "K" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "L" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "M" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "N" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "O" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "P" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "Q" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "R" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3407 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "J" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3440 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Time building chain proxies: 6.90, per 1000 atoms: 0.53 Number of scatterers: 12935 At special positions: 0 Unit cell: (128.1, 130.2, 112.35, 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 10 16.00 P 334 15.00 O 3076 8.00 N 2430 7.00 C 7085 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: 7.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 70.7% alpha, 2.6% beta 167 base pairs and 283 stacking pairs defined. Time for finding SS restraints: 6.96 Creating SS restraints... Processing helix chain 'K' and resid 44 through 57 Processing helix chain 'K' and resid 63 through 79 removed outlier: 3.741A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.774A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 3.907A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.399A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 88 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'N' and resid 37 through 49 Processing helix chain 'N' and resid 55 through 84 Processing helix chain 'N' and resid 90 through 102 Processing helix chain 'N' and resid 104 through 123 Processing helix chain 'O' and resid 44 through 57 Processing helix chain 'O' and resid 63 through 76 removed outlier: 3.579A pdb=" N PHE O 67 " --> pdb=" O ARG O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 removed outlier: 3.994A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 29 Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 4.060A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP P 68 " --> pdb=" O ASN P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 removed outlier: 3.765A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 22 Processing helix chain 'Q' and resid 26 through 37 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.173A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 89 removed outlier: 3.536A pdb=" N ASN Q 89 " --> pdb=" O LEU Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'Q' and resid 112 through 116 Processing helix chain 'R' and resid 37 through 49 Processing helix chain 'R' and resid 55 through 84 Processing helix chain 'R' and resid 90 through 102 Processing helix chain 'R' and resid 104 through 124 Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.933A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'L' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.321A pdb=" N ARG M 42 " --> pdb=" O ILE N 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'M' and resid 100 through 102 removed outlier: 6.465A pdb=" N THR M 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.779A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.350A pdb=" N ARG Q 42 " --> pdb=" O ILE R 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 401 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 427 hydrogen bonds 854 hydrogen bond angles 0 basepair planarities 167 basepair parallelities 283 stacking parallelities Total time for adding SS restraints: 7.01 Time building geometry restraints manager: 8.23 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: 2762 1.33 - 1.46: 4906 1.46 - 1.58: 5494 1.58 - 1.70: 666 1.70 - 1.83: 20 Bond restraints: 13848 Sorted by residual: bond pdb=" O3' DC I 563 " pdb=" P DT I 564 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.50e-02 4.44e+03 1.47e+01 bond pdb=" CB MET N 59 " pdb=" CG MET N 59 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 3.96e+00 bond pdb=" C3' DG J 316 " pdb=" O3' DG J 316 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.67e+00 bond pdb=" C3' DC J 238 " pdb=" O3' DC J 238 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.45e+00 bond pdb=" C3' DC I 430 " pdb=" O3' DC I 430 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.14e+00 ... (remaining 13843 not shown) Histogram of bond angle deviations from ideal: 97.30 - 104.41: 1332 104.41 - 111.52: 6980 111.52 - 118.63: 4135 118.63 - 125.74: 6619 125.74 - 132.85: 1069 Bond angle restraints: 20135 Sorted by residual: angle pdb=" O3' DC I 562 " pdb=" C3' DC I 562 " pdb=" C2' DC I 562 " ideal model delta sigma weight residual 111.50 120.57 -9.07 1.50e+00 4.44e-01 3.65e+01 angle pdb=" N GLU Q 61 " pdb=" CA GLU Q 61 " pdb=" CB GLU Q 61 " ideal model delta sigma weight residual 110.28 118.22 -7.94 1.55e+00 4.16e-01 2.62e+01 angle pdb=" N GLU O 97 " pdb=" CA GLU O 97 " pdb=" CB GLU O 97 " ideal model delta sigma weight residual 110.28 115.93 -5.65 1.55e+00 4.16e-01 1.33e+01 angle pdb=" CA MET N 59 " pdb=" CB MET N 59 " pdb=" CG MET N 59 " ideal model delta sigma weight residual 114.10 106.93 7.17 2.00e+00 2.50e-01 1.29e+01 angle pdb=" C3' DG J 316 " pdb=" O3' DG J 316 " pdb=" P DG J 317 " ideal model delta sigma weight residual 120.20 125.47 -5.27 1.50e+00 4.44e-01 1.23e+01 ... (remaining 20130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.49: 5567 34.49 - 68.98: 1838 68.98 - 103.47: 55 103.47 - 137.96: 3 137.96 - 172.46: 1 Dihedral angle restraints: 7464 sinusoidal: 5242 harmonic: 2222 Sorted by residual: dihedral pdb=" CA PRO R 103 " pdb=" C PRO R 103 " pdb=" N GLY R 104 " pdb=" CA GLY R 104 " ideal model delta harmonic sigma weight residual 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ILE L 50 " pdb=" C ILE L 50 " pdb=" N TYR L 51 " pdb=" CA TYR L 51 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C4' DG J 316 " pdb=" C3' DG J 316 " pdb=" O3' DG J 316 " pdb=" P DG J 317 " ideal model delta sinusoidal sigma weight residual 220.00 47.54 172.46 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1726 0.053 - 0.106: 475 0.106 - 0.160: 71 0.160 - 0.213: 15 0.213 - 0.266: 1 Chirality restraints: 2288 Sorted by residual: chirality pdb=" C3' DC I 562 " pdb=" C4' DC I 562 " pdb=" O3' DC I 562 " pdb=" C2' DC I 562 " both_signs ideal model delta sigma weight residual False -2.66 -2.39 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB THR P 54 " pdb=" CA THR P 54 " pdb=" OG1 THR P 54 " pdb=" CG2 THR P 54 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C4' DA I 439 " pdb=" C5' DA I 439 " pdb=" O4' DA I 439 " pdb=" C3' DA I 439 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2285 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU R 113 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" CD GLU R 113 " -0.067 2.00e-02 2.50e+03 pdb=" OE1 GLU R 113 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU R 113 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 560 " 0.047 2.00e-02 2.50e+03 2.08e-02 1.19e+01 pdb=" N9 DA I 560 " -0.045 2.00e-02 2.50e+03 pdb=" C8 DA I 560 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DA I 560 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA I 560 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 560 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 560 " 0.016 2.00e-02 2.50e+03 pdb=" N1 DA I 560 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 560 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DA I 560 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 560 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 104 " 0.013 2.00e-02 2.50e+03 2.00e-02 7.00e+00 pdb=" CG PHE K 104 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE K 104 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE K 104 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE K 104 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE K 104 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE K 104 " -0.002 2.00e-02 2.50e+03 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3108 2.81 - 3.33: 12445 3.33 - 3.85: 28738 3.85 - 4.38: 31734 4.38 - 4.90: 43238 Nonbonded interactions: 119263 Sorted by model distance: nonbonded pdb=" O VAL N 118 " pdb=" OG1 THR N 122 " model vdw 2.286 2.440 nonbonded pdb=" O THR Q 16 " pdb=" OG SER Q 19 " model vdw 2.296 2.440 nonbonded pdb=" OD1 ASP K 123 " pdb=" NE2 HIS O 113 " model vdw 2.300 2.520 nonbonded pdb=" O GLN K 55 " pdb=" NH2 ARG Q 81 " model vdw 2.308 2.520 nonbonded pdb=" NH2 ARG M 81 " pdb=" O GLN O 55 " model vdw 2.311 2.520 ... (remaining 119258 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 'K' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'R' } 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 6.170 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 45.890 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13848 Z= 0.336 Angle : 0.921 10.019 20135 Z= 0.532 Chirality : 0.050 0.266 2288 Planarity : 0.007 0.071 1390 Dihedral : 30.348 172.456 6032 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -0.07 (0.28), residues: 752 helix: 0.19 (0.21), residues: 510 sheet: None (None), residues: 0 loop : -0.28 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS N 109 PHE 0.045 0.004 PHE K 104 TYR 0.033 0.003 TYR O 54 ARG 0.011 0.001 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9229 (m-80) cc_final: 0.8907 (m-80) REVERT: N 109 HIS cc_start: 0.9687 (m-70) cc_final: 0.9380 (m90) REVERT: R 102 LEU cc_start: 0.8679 (tp) cc_final: 0.8386 (tp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2241 time to fit residues: 30.0084 Evaluate side-chains 62 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 HIS O 76 GLN R 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13848 Z= 0.258 Angle : 0.673 6.420 20135 Z= 0.406 Chirality : 0.037 0.152 2288 Planarity : 0.005 0.059 1390 Dihedral : 33.640 167.807 4508 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.16 % Allowed : 2.20 % Favored : 97.64 % 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: 0.93 (0.30), residues: 752 helix: 0.97 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.09 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS R 109 PHE 0.015 0.002 PHE N 65 TYR 0.015 0.002 TYR R 40 ARG 0.006 0.001 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9206 (m-80) cc_final: 0.8983 (m-80) REVERT: N 109 HIS cc_start: 0.9614 (m90) cc_final: 0.9341 (m90) REVERT: Q 26 PRO cc_start: 0.7564 (Cg_endo) cc_final: 0.7336 (Cg_exo) REVERT: R 102 LEU cc_start: 0.8486 (tp) cc_final: 0.8174 (tp) REVERT: R 109 HIS cc_start: 0.9588 (m-70) cc_final: 0.9119 (m-70) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.2118 time to fit residues: 26.3828 Evaluate side-chains 57 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN O 125 GLN Q 94 ASN Q 112 GLN R 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13848 Z= 0.346 Angle : 0.751 6.840 20135 Z= 0.446 Chirality : 0.041 0.172 2288 Planarity : 0.006 0.064 1390 Dihedral : 34.267 170.880 4508 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 31.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.16 % Allowed : 3.14 % Favored : 96.70 % 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: 0.61 (0.29), residues: 752 helix: 0.80 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -0.33 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS R 109 PHE 0.040 0.003 PHE K 104 TYR 0.015 0.002 TYR N 40 ARG 0.010 0.001 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 104 PHE cc_start: 0.9539 (m-80) cc_final: 0.9287 (m-80) REVERT: K 108 ASN cc_start: 0.9188 (t0) cc_final: 0.8605 (p0) REVERT: Q 26 PRO cc_start: 0.7518 (Cg_endo) cc_final: 0.7187 (Cg_exo) REVERT: R 102 LEU cc_start: 0.8453 (tp) cc_final: 0.8131 (tp) REVERT: R 105 GLU cc_start: 0.9588 (tp30) cc_final: 0.9372 (tp30) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.2130 time to fit residues: 27.0761 Evaluate side-chains 56 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 27 optimal weight: 0.0870 chunk 83 optimal weight: 5.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 55 GLN ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN ** R 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13848 Z= 0.219 Angle : 0.650 5.729 20135 Z= 0.392 Chirality : 0.037 0.160 2288 Planarity : 0.004 0.059 1390 Dihedral : 33.843 169.529 4508 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.30), residues: 752 helix: 1.24 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.05 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS R 109 PHE 0.014 0.002 PHE K 104 TYR 0.013 0.001 TYR N 42 ARG 0.004 0.000 ARG O 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 104 PHE cc_start: 0.9507 (m-80) cc_final: 0.9284 (m-80) REVERT: K 108 ASN cc_start: 0.9123 (t0) cc_final: 0.8443 (p0) REVERT: Q 26 PRO cc_start: 0.7197 (Cg_endo) cc_final: 0.6785 (Cg_exo) REVERT: R 102 LEU cc_start: 0.8552 (tp) cc_final: 0.8284 (tp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2209 time to fit residues: 27.4272 Evaluate side-chains 60 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 76 GLN O 108 ASN Q 94 ASN ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13848 Z= 0.292 Angle : 0.688 5.647 20135 Z= 0.413 Chirality : 0.039 0.164 2288 Planarity : 0.005 0.059 1390 Dihedral : 34.048 167.309 4508 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 28.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.30), residues: 752 helix: 1.16 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.24 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS R 109 PHE 0.030 0.002 PHE O 104 TYR 0.014 0.002 TYR N 40 ARG 0.004 0.001 ARG R 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 51 ILE cc_start: 0.9207 (mm) cc_final: 0.8972 (mm) REVERT: K 54 TYR cc_start: 0.9326 (m-80) cc_final: 0.9046 (m-80) REVERT: Q 26 PRO cc_start: 0.7383 (Cg_endo) cc_final: 0.6994 (Cg_exo) REVERT: R 102 LEU cc_start: 0.8593 (tp) cc_final: 0.8298 (tp) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2295 time to fit residues: 27.9661 Evaluate side-chains 56 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 47 GLN N 95 GLN ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 13848 Z= 0.358 Angle : 0.762 8.477 20135 Z= 0.450 Chirality : 0.042 0.207 2288 Planarity : 0.006 0.058 1390 Dihedral : 34.554 166.559 4508 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 34.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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 (0.29), residues: 752 helix: 0.50 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -0.47 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS R 109 PHE 0.018 0.002 PHE O 67 TYR 0.015 0.002 TYR N 40 ARG 0.007 0.001 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 26 PRO cc_start: 0.7456 (Cg_endo) cc_final: 0.7068 (Cg_exo) REVERT: R 102 LEU cc_start: 0.8624 (tp) cc_final: 0.8331 (tp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2251 time to fit residues: 28.1475 Evaluate side-chains 59 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 59 optimal weight: 7.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13848 Z= 0.209 Angle : 0.671 8.437 20135 Z= 0.400 Chirality : 0.039 0.166 2288 Planarity : 0.004 0.057 1390 Dihedral : 34.015 163.548 4508 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 0.98 (0.29), residues: 752 helix: 1.09 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.31 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS R 49 PHE 0.030 0.002 PHE K 104 TYR 0.010 0.001 TYR P 72 ARG 0.004 0.000 ARG O 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LEU cc_start: 0.9668 (tt) cc_final: 0.9339 (mm) REVERT: Q 26 PRO cc_start: 0.7124 (Cg_endo) cc_final: 0.6698 (Cg_exo) REVERT: Q 64 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9095 (mm-30) REVERT: R 102 LEU cc_start: 0.8455 (tp) cc_final: 0.8177 (tp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2243 time to fit residues: 27.4684 Evaluate side-chains 56 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 68 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 76 GLN O 108 ASN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13848 Z= 0.291 Angle : 0.698 6.604 20135 Z= 0.415 Chirality : 0.039 0.173 2288 Planarity : 0.005 0.059 1390 Dihedral : 34.302 162.052 4508 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 28.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 0.80 (0.30), residues: 752 helix: 0.95 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.35 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS R 109 PHE 0.029 0.002 PHE O 104 TYR 0.014 0.002 TYR N 40 ARG 0.005 0.001 ARG O 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 104 PHE cc_start: 0.9502 (m-10) cc_final: 0.9271 (m-80) REVERT: Q 26 PRO cc_start: 0.7320 (Cg_endo) cc_final: 0.6900 (Cg_exo) REVERT: R 102 LEU cc_start: 0.8475 (tp) cc_final: 0.8171 (tp) REVERT: R 108 LYS cc_start: 0.9769 (ptpp) cc_final: 0.9548 (ptpt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2209 time to fit residues: 24.3600 Evaluate side-chains 59 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 40 optimal weight: 0.0170 chunk 73 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 overall best weight: 5.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 GLN ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.7503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 13848 Z= 0.352 Angle : 0.770 7.205 20135 Z= 0.453 Chirality : 0.042 0.167 2288 Planarity : 0.006 0.055 1390 Dihedral : 34.916 158.936 4508 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 35.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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 (0.29), residues: 752 helix: 0.41 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -0.39 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS K 113 PHE 0.028 0.002 PHE O 104 TYR 0.021 0.002 TYR R 37 ARG 0.006 0.001 ARG M 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 104 PHE cc_start: 0.9460 (m-10) cc_final: 0.9228 (m-80) REVERT: Q 26 PRO cc_start: 0.7357 (Cg_endo) cc_final: 0.6944 (Cg_exo) REVERT: R 57 LYS cc_start: 0.8300 (ptmm) cc_final: 0.7977 (ptmm) REVERT: R 59 MET cc_start: 0.8012 (tpp) cc_final: 0.7656 (tpt) REVERT: R 102 LEU cc_start: 0.8473 (tp) cc_final: 0.8231 (tp) REVERT: R 108 LYS cc_start: 0.9743 (ptpp) cc_final: 0.9530 (ptpt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2571 time to fit residues: 28.2467 Evaluate side-chains 58 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 87 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 ASN ** R 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.7428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13848 Z= 0.224 Angle : 0.683 7.922 20135 Z= 0.407 Chirality : 0.039 0.154 2288 Planarity : 0.004 0.057 1390 Dihedral : 34.341 156.893 4508 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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 (0.29), residues: 752 helix: 0.88 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.43 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 49 PHE 0.026 0.002 PHE O 104 TYR 0.012 0.001 TYR R 40 ARG 0.007 0.000 ARG O 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LEU cc_start: 0.9673 (tp) cc_final: 0.9463 (pp) REVERT: K 54 TYR cc_start: 0.9410 (m-10) cc_final: 0.9159 (m-80) REVERT: O 54 TYR cc_start: 0.8713 (m-10) cc_final: 0.8484 (m-80) REVERT: Q 26 PRO cc_start: 0.7519 (Cg_endo) cc_final: 0.7128 (Cg_exo) REVERT: Q 64 GLU cc_start: 0.9549 (mm-30) cc_final: 0.9218 (mm-30) REVERT: R 57 LYS cc_start: 0.8054 (ptmm) cc_final: 0.7795 (ptmt) REVERT: R 59 MET cc_start: 0.8227 (tpp) cc_final: 0.7877 (tpt) REVERT: R 102 LEU cc_start: 0.8388 (tp) cc_final: 0.8142 (tp) REVERT: R 109 HIS cc_start: 0.9421 (m90) cc_final: 0.9173 (m-70) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2367 time to fit residues: 28.1484 Evaluate side-chains 59 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 34 optimal weight: 0.0570 chunk 84 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN O 108 ASN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.031045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.025962 restraints weight = 222027.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.026757 restraints weight = 128896.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.027298 restraints weight = 85829.065| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.7726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13848 Z= 0.279 Angle : 0.702 7.831 20135 Z= 0.416 Chirality : 0.039 0.190 2288 Planarity : 0.005 0.057 1390 Dihedral : 34.522 154.627 4508 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 27.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: 0.66 (0.30), residues: 752 helix: 0.86 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.42 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS R 109 PHE 0.059 0.003 PHE K 104 TYR 0.014 0.002 TYR R 37 ARG 0.004 0.001 ARG Q 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1801.77 seconds wall clock time: 34 minutes 13.08 seconds (2053.08 seconds total)