Starting phenix.real_space_refine on Thu Nov 16 10:27:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pff_13374/11_2023/7pff_13374.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pff_13374/11_2023/7pff_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_13374/11_2023/7pff_13374.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pff_13374/11_2023/7pff_13374.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pff_13374/11_2023/7pff_13374.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pff_13374/11_2023/7pff_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 6.51, per 1000 atoms: 0.50 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: 7.40 Conformation dependent library (CDL) restraints added in 1.0 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: 6.93 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: 6.77 Time building geometry restraints manager: 7.71 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: 5344 34.49 - 68.98: 1765 68.98 - 103.47: 55 103.47 - 137.96: 3 137.96 - 172.46: 1 Dihedral angle restraints: 7168 sinusoidal: 4946 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 7165 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: 1.410 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: 6.070 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 43.960 Find NCS groups from input model: 0.480 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.370 ------------------------------------------------------------------------------- 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 : 30.382 172.456 5736 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 *********************** 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 : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2319 time to fit residues: 31.1625 Evaluate side-chains 60 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1507 ------------------------------------------------------------------------------- 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: 0.7980 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- 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** O 76 GLN R 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1472 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= 0.231 Angle : 0.656 5.561 20135 Z= 0.396 Chirality : 0.036 0.151 2288 Planarity : 0.005 0.061 1390 Dihedral : 34.069 168.347 4212 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.16 % Allowed : 1.73 % Favored : 98.11 % 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 (0.30), residues: 752 helix: 1.00 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.03 (0.41), residues: 208 *********************** 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 82 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.2312 time to fit residues: 29.0545 Evaluate side-chains 52 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2115 ------------------------------------------------------------------------------- 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: 5.9990 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 47 GLN ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8217 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 13848 Z= 0.410 Angle : 0.804 8.362 20135 Z= 0.476 Chirality : 0.043 0.184 2288 Planarity : 0.007 0.067 1390 Dihedral : 35.122 171.468 4212 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 37.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.16 % Allowed : 3.77 % 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: 0.34 (0.29), residues: 752 helix: 0.55 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -0.30 (0.41), residues: 226 *********************** 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 77 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.2397 time to fit residues: 28.0607 Evaluate side-chains 47 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1389 ------------------------------------------------------------------------------- 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: 6.9990 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 27 optimal weight: 0.0010 chunk 83 optimal weight: 5.9990 overall best weight: 3.9994 ------------------------------------------------------------------------------- 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: 0.8158 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13848 Z= 0.289 Angle : 0.703 5.632 20135 Z= 0.422 Chirality : 0.039 0.180 2288 Planarity : 0.005 0.060 1390 Dihedral : 34.804 170.074 4212 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 25.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: 0.79 (0.30), residues: 752 helix: 0.91 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -0.21 (0.41), residues: 220 *********************** 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 80 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2293 time to fit residues: 28.0641 Evaluate side-chains 55 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1027 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 33 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: N 95 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: 0.8235 moved from start: 0.5323 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= 0.344 Angle : 0.748 6.518 20135 Z= 0.444 Chirality : 0.041 0.193 2288 Planarity : 0.006 0.061 1390 Dihedral : 35.180 168.098 4212 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 34.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % 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: 0.47 (0.29), residues: 752 helix: 0.72 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.42 (0.41), residues: 226 *********************** 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 : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2443 time to fit residues: 28.8878 Evaluate side-chains 55 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0880 ------------------------------------------------------------------------------- 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: 6.9990 chunk 19 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 overall best weight: 3.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5486 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= 0.261 Angle : 0.690 5.809 20135 Z= 0.414 Chirality : 0.039 0.179 2288 Planarity : 0.005 0.062 1390 Dihedral : 34.956 167.179 4212 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 25.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % 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: 0.76 (0.30), residues: 752 helix: 0.94 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.43 (0.42), residues: 210 *********************** 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 74 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2390 time to fit residues: 27.1180 Evaluate side-chains 56 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1487 ------------------------------------------------------------------------------- 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: 0.3980 chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 GLN ** N 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8165 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13848 Z= 0.247 Angle : 0.686 6.976 20135 Z= 0.410 Chirality : 0.038 0.175 2288 Planarity : 0.005 0.061 1390 Dihedral : 34.933 165.462 4212 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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 (0.30), residues: 752 helix: 1.09 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.29 (0.42), residues: 214 *********************** 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 78 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2300 time to fit residues: 27.3058 Evaluate side-chains 58 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1027 ------------------------------------------------------------------------------- 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: 5.9990 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 78 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 68 GLN ** N 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN O 108 ASN ** R 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13848 Z= 0.221 Angle : 0.669 9.773 20135 Z= 0.400 Chirality : 0.038 0.166 2288 Planarity : 0.004 0.057 1390 Dihedral : 34.749 163.341 4212 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: 1.13 (0.30), residues: 752 helix: 1.21 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.25 (0.41), residues: 216 *********************** 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 79 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2477 time to fit residues: 29.2478 Evaluate side-chains 58 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1648 ------------------------------------------------------------------------------- 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: 4.9990 chunk 40 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 HIS Q 84 GLN ** 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: 0.8236 moved from start: 0.6830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13848 Z= 0.333 Angle : 0.742 7.183 20135 Z= 0.439 Chirality : 0.041 0.181 2288 Planarity : 0.006 0.066 1390 Dihedral : 35.331 161.574 4212 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 32.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.30), residues: 752 helix: 0.77 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.36 (0.42), residues: 218 *********************** 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 76 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2399 time to fit residues: 27.6490 Evaluate side-chains 60 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1577 ------------------------------------------------------------------------------- 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: 5.9990 chunk 103 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.7557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13848 Z= 0.310 Angle : 0.734 8.636 20135 Z= 0.436 Chirality : 0.040 0.168 2288 Planarity : 0.005 0.065 1390 Dihedral : 35.336 158.055 4212 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 30.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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: 0.39 (0.30), residues: 752 helix: 0.64 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.44 (0.42), residues: 218 ********************** 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 76 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2360 time to fit residues: 27.2793 Evaluate side-chains 60 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0847 ------------------------------------------------------------------------------- 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: 5.9990 chunk 22 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.030322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.025248 restraints weight = 225566.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.026042 restraints weight = 130275.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.026567 restraints weight = 86497.583| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.7894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13848 Z= 0.300 Angle : 0.722 6.801 20135 Z= 0.428 Chirality : 0.040 0.189 2288 Planarity : 0.005 0.060 1390 Dihedral : 35.414 156.020 4212 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 29.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % 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: 0.49 (0.30), residues: 752 helix: 0.74 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.50 (0.42), residues: 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1775.07 seconds wall clock time: 34 minutes 4.51 seconds (2044.51 seconds total)