Starting phenix.real_space_refine on Sat Dec 9 20:46:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl9_36389/12_2023/8jl9_36389.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl9_36389/12_2023/8jl9_36389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl9_36389/12_2023/8jl9_36389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl9_36389/12_2023/8jl9_36389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl9_36389/12_2023/8jl9_36389.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl9_36389/12_2023/8jl9_36389.pdb" } resolution = 2.65 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= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 310 5.49 5 S 14 5.16 5 C 6763 2.51 5 N 2312 2.21 5 O 2915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 59": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12314 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3178 Classifications: {'DNA': 155} Link IDs: {'rna3p': 154} Chain: "J" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3177 Classifications: {'DNA': 155} Link IDs: {'rna3p': 154} Time building chain proxies: 6.31, per 1000 atoms: 0.51 Number of scatterers: 12314 At special positions: 0 Unit cell: (74.2, 120.84, 129.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 310 15.00 O 2915 8.00 N 2312 7.00 C 6763 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: 5.72 Conformation dependent library (CDL) restraints added in 1.0 seconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.4% alpha, 3.2% beta 155 base pairs and 283 stacking pairs defined. Time for finding SS restraints: 6.34 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.932A 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 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.656A 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 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.481A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.504A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.973A 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 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.671A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (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 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.474A 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 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.897A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.277A 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 100 through 102 removed outlier: 6.329A 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: 6.914A 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: 7.126A 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 78 412 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 398 hydrogen bonds 796 hydrogen bond angles 0 basepair planarities 155 basepair parallelities 283 stacking parallelities Total time for adding SS restraints: 4.97 Time building geometry restraints manager: 6.09 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: 2146 1.33 - 1.45: 4427 1.45 - 1.57: 5950 1.57 - 1.69: 619 1.69 - 1.81: 24 Bond restraints: 13166 Sorted by residual: bond pdb=" C SER D 32 " pdb=" N ARG D 33 " ideal model delta sigma weight residual 1.330 1.257 0.073 1.39e-02 5.18e+03 2.73e+01 bond pdb=" CZ ARG E 131 " pdb=" NH2 ARG E 131 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.22e+01 bond pdb=" CZ ARG G 88 " pdb=" NH2 ARG G 88 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" CZ ARG E 116 " pdb=" NH2 ARG E 116 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.45e+00 bond pdb=" CZ ARG D 72 " pdb=" NH2 ARG D 72 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.27e+00 ... (remaining 13161 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.11: 1333 105.11 - 112.01: 6999 112.01 - 118.91: 3612 118.91 - 125.81: 6128 125.81 - 132.71: 1040 Bond angle restraints: 19112 Sorted by residual: angle pdb=" C SER D 32 " pdb=" CA SER D 32 " pdb=" CB SER D 32 " ideal model delta sigma weight residual 110.42 121.67 -11.25 1.99e+00 2.53e-01 3.20e+01 angle pdb=" O SER D 32 " pdb=" C SER D 32 " pdb=" N ARG D 33 " ideal model delta sigma weight residual 122.59 116.13 6.46 1.33e+00 5.65e-01 2.36e+01 angle pdb=" CA PRO A 38 " pdb=" N PRO A 38 " pdb=" CD PRO A 38 " ideal model delta sigma weight residual 112.00 106.41 5.59 1.40e+00 5.10e-01 1.60e+01 angle pdb=" CA ILE H 61 " pdb=" CB ILE H 61 " pdb=" CG1 ILE H 61 " ideal model delta sigma weight residual 110.40 117.02 -6.62 1.70e+00 3.46e-01 1.52e+01 angle pdb=" CD ARG E 131 " pdb=" NE ARG E 131 " pdb=" CZ ARG E 131 " ideal model delta sigma weight residual 124.40 129.82 -5.42 1.40e+00 5.10e-01 1.50e+01 ... (remaining 19107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.16: 5357 32.16 - 64.31: 1688 64.31 - 96.47: 53 96.47 - 128.63: 0 128.63 - 160.79: 2 Dihedral angle restraints: 7100 sinusoidal: 4927 harmonic: 2173 Sorted by residual: dihedral pdb=" C SER D 32 " pdb=" N SER D 32 " pdb=" CA SER D 32 " pdb=" CB SER D 32 " ideal model delta harmonic sigma weight residual -122.60 -140.37 17.77 0 2.50e+00 1.60e-01 5.05e+01 dihedral pdb=" N SER D 32 " pdb=" C SER D 32 " pdb=" CA SER D 32 " pdb=" CB SER D 32 " ideal model delta harmonic sigma weight residual 122.80 135.82 -13.02 0 2.50e+00 1.60e-01 2.71e+01 dihedral pdb=" CA ARG D 33 " pdb=" C ARG D 33 " pdb=" N LYS D 34 " pdb=" CA LYS D 34 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 7097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2123 0.119 - 0.238: 41 0.238 - 0.357: 6 0.357 - 0.476: 0 0.476 - 0.595: 1 Chirality restraints: 2171 Sorted by residual: chirality pdb=" CA SER D 32 " pdb=" N SER D 32 " pdb=" C SER D 32 " pdb=" CB SER D 32 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.60 2.00e-01 2.50e+01 8.86e+00 chirality pdb=" CA PRO B 32 " pdb=" N PRO B 32 " pdb=" C PRO B 32 " pdb=" CB PRO B 32 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA PRO F 32 " pdb=" N PRO F 32 " pdb=" C PRO F 32 " pdb=" CB PRO F 32 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 2168 not shown) Planarity restraints: 1347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 40 " -0.099 2.00e-02 2.50e+03 5.09e-02 5.18e+01 pdb=" CG TYR D 40 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR D 40 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR D 40 " 0.057 2.00e-02 2.50e+03 pdb=" CE1 TYR D 40 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR D 40 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 40 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR D 40 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 17 " -0.531 9.50e-02 1.11e+02 2.38e-01 3.48e+01 pdb=" NE ARG G 17 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG G 17 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG G 17 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 17 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -76 " 0.052 2.00e-02 2.50e+03 2.80e-02 1.96e+01 pdb=" N1 DT I -76 " -0.070 2.00e-02 2.50e+03 pdb=" C2 DT I -76 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DT I -76 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT I -76 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DT I -76 " 0.008 2.00e-02 2.50e+03 pdb=" O4 DT I -76 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DT I -76 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I -76 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT I -76 " -0.005 2.00e-02 2.50e+03 ... (remaining 1344 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 8 2.47 - 3.08: 7511 3.08 - 3.69: 20503 3.69 - 4.29: 32533 4.29 - 4.90: 46271 Nonbonded interactions: 106826 Sorted by model distance: nonbonded pdb=" OD2 ASP F 68 " pdb=" NH1 ARG F 92 " model vdw 1.865 2.520 nonbonded pdb=" NH2 ARG F 92 " pdb=" O LEU H 100 " model vdw 2.337 2.520 nonbonded pdb=" O HIS F 75 " pdb=" NH1 ARG H 92 " model vdw 2.399 2.520 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.403 2.440 nonbonded pdb=" O ASN D 67 " pdb=" OE1 GLU D 71 " model vdw 2.403 3.040 ... (remaining 106821 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' and resid 39 through 133) 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' } ncs_group { reference = (chain 'I' and (resid -77 through -1 or resid 1 through 77)) selection = (chain 'J' and (resid -77 through -1 or resid 1 through 77)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.390 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 38.950 Find NCS groups from input model: 0.540 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: 0.000 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 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 : 0.005 0.111 13166 Z= 0.322 Angle : 0.857 11.254 19112 Z= 0.565 Chirality : 0.048 0.595 2171 Planarity : 0.012 0.238 1347 Dihedral : 28.861 160.785 5702 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Cbeta Deviations : 0.14 % 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: 0.24 (0.27), residues: 737 helix: 0.48 (0.20), residues: 532 sheet: None (None), residues: 0 loop : -0.40 (0.37), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 109 PHE 0.012 0.002 PHE A 84 TYR 0.099 0.004 TYR D 40 ARG 0.005 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.781 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 146 average time/residue: 1.9954 time to fit residues: 306.4276 Evaluate side-chains 130 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1464 time to fit residues: 1.2185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN A 125 GLN E 68 GLN F 25 ASN F 27 GLN F 93 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13166 Z= 0.262 Angle : 0.588 4.844 19112 Z= 0.363 Chirality : 0.038 0.132 2171 Planarity : 0.004 0.035 1347 Dihedral : 30.288 170.817 4223 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.93 % Allowed : 17.98 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.30), residues: 737 helix: 2.59 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.23 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 109 PHE 0.007 0.001 PHE G 25 TYR 0.012 0.002 TYR H 40 ARG 0.005 0.001 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 0.997 Fit side-chains outliers start: 12 outliers final: 1 residues processed: 125 average time/residue: 2.0701 time to fit residues: 271.8482 Evaluate side-chains 107 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1077 time to fit residues: 1.2615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN F 25 ASN F 75 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 13166 Z= 0.453 Angle : 0.670 5.866 19112 Z= 0.405 Chirality : 0.045 0.161 2171 Planarity : 0.005 0.047 1347 Dihedral : 30.343 172.000 4223 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.57 % Allowed : 18.78 % Favored : 78.65 % 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: 2.42 (0.30), residues: 737 helix: 2.30 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.39 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 113 PHE 0.009 0.002 PHE H 70 TYR 0.018 0.002 TYR D 40 ARG 0.007 0.001 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.885 Fit side-chains outliers start: 16 outliers final: 4 residues processed: 105 average time/residue: 2.4041 time to fit residues: 264.0337 Evaluate side-chains 98 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1055 time to fit residues: 1.2447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 93 GLN F 25 ASN F 93 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13166 Z= 0.268 Angle : 0.614 8.629 19112 Z= 0.381 Chirality : 0.039 0.130 2171 Planarity : 0.005 0.050 1347 Dihedral : 30.358 172.665 4223 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.12 % Allowed : 19.90 % Favored : 78.97 % 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: 2.62 (0.30), residues: 737 helix: 2.45 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.34 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.014 0.001 PHE D 70 TYR 0.014 0.002 TYR D 40 ARG 0.004 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.868 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 96 average time/residue: 2.5157 time to fit residues: 252.1556 Evaluate side-chains 90 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.5100 time to fit residues: 2.6499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 66 optimal weight: 0.0670 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 93 GLN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13166 Z= 0.198 Angle : 0.597 8.314 19112 Z= 0.368 Chirality : 0.036 0.125 2171 Planarity : 0.004 0.046 1347 Dihedral : 30.355 171.922 4223 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.12 % Allowed : 20.55 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.30), residues: 737 helix: 2.64 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.25 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.006 0.001 PHE A 67 TYR 0.012 0.001 TYR H 40 ARG 0.005 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.818 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 93 average time/residue: 2.3623 time to fit residues: 230.0796 Evaluate side-chains 89 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.9715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 93 GLN C 73 ASN F 25 ASN H 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13166 Z= 0.297 Angle : 0.593 7.228 19112 Z= 0.366 Chirality : 0.039 0.131 2171 Planarity : 0.004 0.046 1347 Dihedral : 30.287 171.786 4223 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.12 % Allowed : 21.35 % Favored : 77.53 % 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: 2.78 (0.30), residues: 737 helix: 2.57 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.32 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 113 PHE 0.007 0.001 PHE H 70 TYR 0.013 0.002 TYR D 40 ARG 0.007 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.896 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 99 average time/residue: 2.4256 time to fit residues: 251.2187 Evaluate side-chains 92 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.916 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.0877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 57 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13166 Z= 0.236 Angle : 0.586 7.669 19112 Z= 0.362 Chirality : 0.037 0.122 2171 Planarity : 0.004 0.045 1347 Dihedral : 30.304 171.752 4223 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.96 % Allowed : 21.19 % Favored : 77.85 % 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: 2.87 (0.30), residues: 737 helix: 2.64 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.27 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.005 0.001 PHE A 67 TYR 0.012 0.001 TYR D 40 ARG 0.005 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.915 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 94 average time/residue: 2.3257 time to fit residues: 229.0911 Evaluate side-chains 93 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.779 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.9761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 93 GLN F 25 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13166 Z= 0.326 Angle : 0.605 7.662 19112 Z= 0.371 Chirality : 0.040 0.134 2171 Planarity : 0.005 0.046 1347 Dihedral : 30.262 173.029 4223 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.28 % Allowed : 21.03 % Favored : 77.69 % 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: 2.68 (0.30), residues: 737 helix: 2.49 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.32 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 113 PHE 0.006 0.002 PHE A 84 TYR 0.014 0.002 TYR D 40 ARG 0.004 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.864 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 96 average time/residue: 2.3891 time to fit residues: 240.1864 Evaluate side-chains 95 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.0001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13166 Z= 0.208 Angle : 0.592 8.110 19112 Z= 0.364 Chirality : 0.036 0.125 2171 Planarity : 0.004 0.045 1347 Dihedral : 30.290 172.783 4223 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.12 % Allowed : 21.83 % Favored : 77.05 % 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: 2.83 (0.30), residues: 737 helix: 2.60 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.26 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 113 PHE 0.006 0.001 PHE A 67 TYR 0.012 0.001 TYR D 40 ARG 0.008 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.950 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 96 average time/residue: 2.3982 time to fit residues: 241.0009 Evaluate side-chains 95 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.9846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 93 GLN F 25 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13166 Z= 0.326 Angle : 0.603 9.571 19112 Z= 0.369 Chirality : 0.039 0.133 2171 Planarity : 0.005 0.046 1347 Dihedral : 30.261 172.565 4223 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.96 % Allowed : 21.99 % Favored : 77.05 % 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: 2.64 (0.30), residues: 737 helix: 2.46 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.33 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 113 PHE 0.007 0.002 PHE H 70 TYR 0.014 0.002 TYR D 40 ARG 0.005 0.000 ARG E 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 1.017 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 95 average time/residue: 2.3702 time to fit residues: 236.6465 Evaluate side-chains 95 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.0793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.112156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.097383 restraints weight = 16395.385| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 0.76 r_work: 0.3104 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13166 Z= 0.234 Angle : 0.593 10.123 19112 Z= 0.365 Chirality : 0.036 0.123 2171 Planarity : 0.004 0.045 1347 Dihedral : 30.278 172.247 4223 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.96 % Allowed : 22.31 % Favored : 76.73 % 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: 2.73 (0.30), residues: 737 helix: 2.52 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.28 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.005 0.001 PHE A 67 TYR 0.024 0.002 TYR B 88 ARG 0.006 0.000 ARG E 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4100.12 seconds wall clock time: 73 minutes 46.03 seconds (4426.03 seconds total)