Starting phenix.real_space_refine (version: dev) on Tue Feb 21 23:47:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfv_13381/02_2023/7pfv_13381.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfv_13381/02_2023/7pfv_13381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfv_13381/02_2023/7pfv_13381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfv_13381/02_2023/7pfv_13381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfv_13381/02_2023/7pfv_13381.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfv_13381/02_2023/7pfv_13381.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13880 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" 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: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "J" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3647 Classifications: {'DNA': 177} Link IDs: {'rna3p': 176} Chain: "I" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3610 Classifications: {'DNA': 177} Link IDs: {'rna3p': 176} Chain: "U" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 7.66, per 1000 atoms: 0.55 Number of scatterers: 13880 At special positions: 0 Unit cell: (137.55, 90.3, 139.65, 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 354 15.00 O 3298 8.00 N 2606 7.00 C 7612 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: 8.12 Conformation dependent library (CDL) restraints added in 1.2 seconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 11 sheets defined 70.0% alpha, 3.3% beta 173 base pairs and 312 stacking pairs defined. Time for finding SS restraints: 6.74 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.769A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.704A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.950A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.279A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.534A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.643A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.621A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.125A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.279A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.508A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 49 removed outlier: 3.951A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 69 Processing helix chain 'U' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.746A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.221A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.967A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.490A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.777A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.408A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'U' and resid 56 through 57 437 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 445 hydrogen bonds 890 hydrogen bond angles 0 basepair planarities 173 basepair parallelities 312 stacking parallelities Total time for adding SS restraints: 6.79 Time building geometry restraints manager: 8.42 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: 2439 1.33 - 1.45: 5131 1.45 - 1.57: 6550 1.57 - 1.69: 706 1.69 - 1.81: 20 Bond restraints: 14846 Sorted by residual: bond pdb=" CD GLU A 97 " pdb=" OE1 GLU A 97 " ideal model delta sigma weight residual 1.249 1.211 0.038 1.90e-02 2.77e+03 4.01e+00 bond pdb=" CG GLU A 105 " pdb=" CD GLU A 105 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.94e+00 bond pdb=" CG GLU A 97 " pdb=" CD GLU A 97 " ideal model delta sigma weight residual 1.516 1.467 0.049 2.50e-02 1.60e+03 3.81e+00 bond pdb=" C3' DG I 158 " pdb=" O3' DG I 158 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.69e+00 bond pdb=" CD GLU B 74 " pdb=" OE1 GLU B 74 " ideal model delta sigma weight residual 1.249 1.214 0.035 1.90e-02 2.77e+03 3.36e+00 ... (remaining 14841 not shown) Histogram of bond angle deviations from ideal: 96.48 - 103.74: 1089 103.74 - 111.01: 7008 111.01 - 118.27: 5061 118.27 - 125.54: 7242 125.54 - 132.80: 1163 Bond angle restraints: 21563 Sorted by residual: angle pdb=" CA GLU A 97 " pdb=" CB GLU A 97 " pdb=" CG GLU A 97 " ideal model delta sigma weight residual 114.10 124.88 -10.78 2.00e+00 2.50e-01 2.90e+01 angle pdb=" N GLU A 97 " pdb=" CA GLU A 97 " pdb=" CB GLU A 97 " ideal model delta sigma weight residual 110.39 118.91 -8.52 1.66e+00 3.63e-01 2.63e+01 angle pdb=" N GLU A 105 " pdb=" CA GLU A 105 " pdb=" CB GLU A 105 " ideal model delta sigma weight residual 110.28 117.86 -7.58 1.55e+00 4.16e-01 2.39e+01 angle pdb=" N GLU B 74 " pdb=" CA GLU B 74 " pdb=" CB GLU B 74 " ideal model delta sigma weight residual 110.28 117.50 -7.22 1.55e+00 4.16e-01 2.17e+01 angle pdb=" N GLU A 94 " pdb=" CA GLU A 94 " pdb=" CB GLU A 94 " ideal model delta sigma weight residual 110.22 117.34 -7.12 1.54e+00 4.22e-01 2.14e+01 ... (remaining 21558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 5787 35.35 - 70.70: 1868 70.70 - 106.05: 48 106.05 - 141.40: 2 141.40 - 176.75: 2 Dihedral angle restraints: 7707 sinusoidal: 5276 harmonic: 2431 Sorted by residual: dihedral pdb=" CA PHE A 84 " pdb=" C PHE A 84 " pdb=" N GLN A 85 " pdb=" CA GLN A 85 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ILE F 50 " pdb=" C ILE F 50 " pdb=" N TYR F 51 " pdb=" CA TYR F 51 " ideal model delta harmonic sigma weight residual -180.00 -157.41 -22.59 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 7704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1798 0.046 - 0.092: 526 0.092 - 0.137: 115 0.137 - 0.183: 14 0.183 - 0.229: 3 Chirality restraints: 2456 Sorted by residual: chirality pdb=" CA ARG B 23 " pdb=" N ARG B 23 " pdb=" C ARG B 23 " pdb=" CB ARG B 23 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA GLU H 71 " pdb=" N GLU H 71 " pdb=" C GLU H 71 " pdb=" CB GLU H 71 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA GLU A 97 " pdb=" N GLU A 97 " pdb=" C GLU A 97 " pdb=" CB GLU A 97 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2453 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 101 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.10e+00 pdb=" C VAL A 101 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL A 101 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY A 102 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 70 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C VAL B 70 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL B 70 " 0.019 2.00e-02 2.50e+03 pdb=" N THR B 71 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 61 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" CD GLU C 61 " 0.049 2.00e-02 2.50e+03 pdb=" OE1 GLU C 61 " -0.018 2.00e-02 2.50e+03 pdb=" OE2 GLU C 61 " -0.018 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2905 2.78 - 3.31: 12957 3.31 - 3.84: 30777 3.84 - 4.37: 34193 4.37 - 4.90: 46781 Nonbonded interactions: 127613 Sorted by model distance: nonbonded pdb=" NH1 ARG B 23 " pdb=" OD1 ASP B 24 " model vdw 2.249 2.520 nonbonded pdb=" OD1 ASP A 123 " pdb=" NE2 HIS E 113 " model vdw 2.265 2.520 nonbonded pdb=" OG SER G 40 " pdb=" O ARG G 42 " model vdw 2.273 2.440 nonbonded pdb=" OP1 DT J 649 " pdb=" NH1 ARG U 53 " model vdw 2.277 2.520 nonbonded pdb=" OG SER C 40 " pdb=" O ARG C 42 " model vdw 2.307 2.440 ... (remaining 127608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 354 5.49 5 S 10 5.16 5 C 7612 2.51 5 N 2606 2.21 5 O 3298 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.890 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: 7.010 Check model and map are aligned: 0.160 Process input model: 46.270 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.130 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 0.058 14846 Z= 0.334 Angle : 0.865 10.776 21563 Z= 0.502 Chirality : 0.045 0.229 2456 Planarity : 0.007 0.091 1498 Dihedral : 30.468 176.752 6141 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer Outliers : 0.00 % 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: 0.36 (0.26), residues: 825 helix: 0.67 (0.20), residues: 575 sheet: -2.49 (1.47), residues: 10 loop : -0.45 (0.34), residues: 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.957 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: 101 average time/residue: 0.2882 time to fit residues: 41.3179 Evaluate side-chains 64 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.054 14846 Z= 0.431 Angle : 0.745 7.200 21563 Z= 0.443 Chirality : 0.040 0.173 2456 Planarity : 0.005 0.045 1498 Dihedral : 34.414 174.820 4489 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 28.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer Outliers : 0.43 % 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: 1.30 (0.27), residues: 825 helix: 1.48 (0.20), residues: 576 sheet: -1.99 (1.71), residues: 10 loop : -0.43 (0.35), residues: 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 85 average time/residue: 0.2921 time to fit residues: 35.6312 Evaluate side-chains 53 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1304 time to fit residues: 1.7993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 14846 Z= 0.225 Angle : 0.616 5.735 21563 Z= 0.372 Chirality : 0.035 0.148 2456 Planarity : 0.004 0.043 1498 Dihedral : 34.094 176.290 4489 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer Outliers : 0.14 % 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: 1.95 (0.28), residues: 825 helix: 1.92 (0.21), residues: 590 sheet: -1.80 (1.75), residues: 10 loop : -0.18 (0.37), residues: 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 88 average time/residue: 0.2838 time to fit residues: 36.1719 Evaluate side-chains 59 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1560 time to fit residues: 1.5299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.048 14846 Z= 0.358 Angle : 0.688 6.010 21563 Z= 0.409 Chirality : 0.037 0.157 2456 Planarity : 0.005 0.043 1498 Dihedral : 34.334 178.560 4489 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 28.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 0.14 % 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: 1.69 (0.28), residues: 825 helix: 1.73 (0.21), residues: 588 sheet: -1.77 (1.80), residues: 10 loop : -0.28 (0.37), residues: 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.2862 time to fit residues: 32.1399 Evaluate side-chains 51 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.0010 chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 overall best weight: 3.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 93 GLN E 93 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 14846 Z= 0.243 Angle : 0.623 5.648 21563 Z= 0.375 Chirality : 0.035 0.140 2456 Planarity : 0.004 0.045 1498 Dihedral : 34.081 175.374 4489 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer Outliers : 0.00 % 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: 1.93 (0.28), residues: 825 helix: 1.94 (0.21), residues: 588 sheet: -1.65 (1.78), residues: 10 loop : -0.28 (0.37), residues: 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2763 time to fit residues: 33.2030 Evaluate side-chains 51 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 109 optimal weight: 30.0000 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 0.4980 chunk 9 optimal weight: 0.0970 chunk 36 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 93 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 14846 Z= 0.193 Angle : 0.591 5.983 21563 Z= 0.355 Chirality : 0.034 0.136 2456 Planarity : 0.004 0.046 1498 Dihedral : 33.574 167.768 4489 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.29), residues: 825 helix: 2.17 (0.21), residues: 580 sheet: -1.41 (1.78), residues: 10 loop : -0.23 (0.37), residues: 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2759 time to fit residues: 36.7882 Evaluate side-chains 56 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 108 optimal weight: 30.0000 chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 93 GLN B 25 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 14846 Z= 0.225 Angle : 0.602 6.719 21563 Z= 0.362 Chirality : 0.034 0.184 2456 Planarity : 0.004 0.044 1498 Dihedral : 33.600 173.476 4489 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.29), residues: 825 helix: 2.17 (0.21), residues: 582 sheet: -1.24 (1.80), residues: 10 loop : -0.14 (0.38), residues: 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2920 time to fit residues: 36.2392 Evaluate side-chains 57 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 93 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.038 14846 Z= 0.298 Angle : 0.647 6.699 21563 Z= 0.387 Chirality : 0.036 0.165 2456 Planarity : 0.004 0.044 1498 Dihedral : 33.969 179.749 4489 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 25.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.00 % 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: 1.99 (0.29), residues: 825 helix: 2.01 (0.21), residues: 578 sheet: -1.29 (1.81), residues: 10 loop : -0.25 (0.38), residues: 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.014 Fit side-chains revert: symmetry clash 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: 0.2766 time to fit residues: 32.5104 Evaluate side-chains 53 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 93 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 14846 Z= 0.259 Angle : 0.631 5.837 21563 Z= 0.377 Chirality : 0.035 0.150 2456 Planarity : 0.004 0.043 1498 Dihedral : 33.925 177.957 4489 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.29), residues: 825 helix: 2.24 (0.21), residues: 566 sheet: -1.21 (1.79), residues: 10 loop : -0.34 (0.37), residues: 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2617 time to fit residues: 32.2850 Evaluate side-chains 52 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 112 optimal weight: 0.3980 chunk 103 optimal weight: 7.9990 chunk 89 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 93 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 14846 Z= 0.258 Angle : 0.637 7.335 21563 Z= 0.380 Chirality : 0.035 0.205 2456 Planarity : 0.004 0.046 1498 Dihedral : 33.931 178.414 4489 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.29), residues: 825 helix: 2.05 (0.21), residues: 578 sheet: -1.15 (1.81), residues: 10 loop : -0.28 (0.38), residues: 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2699 time to fit residues: 31.9570 Evaluate side-chains 52 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 93 GLN ** G 24 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 = 0.2908 r_free = 0.2908 target = 0.028751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.022217 restraints weight = 220795.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.022942 restraints weight = 106785.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.023380 restraints weight = 64170.794| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 14846 Z= 0.190 Angle : 0.602 5.950 21563 Z= 0.359 Chirality : 0.034 0.159 2456 Planarity : 0.005 0.097 1498 Dihedral : 33.536 178.395 4489 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.29), residues: 825 helix: 2.27 (0.22), residues: 580 sheet: -0.93 (1.79), residues: 10 loop : -0.20 (0.39), residues: 235 =============================================================================== Job complete usr+sys time: 1762.01 seconds wall clock time: 33 minutes 31.75 seconds (2011.75 seconds total)