Starting phenix.real_space_refine on Fri Dec 8 16:20:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etv_28600/12_2023/8etv_28600_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etv_28600/12_2023/8etv_28600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etv_28600/12_2023/8etv_28600.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etv_28600/12_2023/8etv_28600.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etv_28600/12_2023/8etv_28600_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etv_28600/12_2023/8etv_28600_neut.pdb" } resolution = 3.16 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= 0.000 sd= 0.011 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 218 5.49 5 S 8 5.16 5 C 4769 2.51 5 N 1634 2.21 5 O 2053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 8682 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "B" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 813 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} 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: "I" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2240 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Chain: "J" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2264 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Time building chain proxies: 5.15, per 1000 atoms: 0.59 Number of scatterers: 8682 At special positions: 0 Unit cell: (117.735, 103.54, 105.21, 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 8 16.00 P 218 15.00 O 2053 8.00 N 1634 7.00 C 4769 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: 4.60 Conformation dependent library (CDL) restraints added in 1.0 seconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 986 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 7 sheets defined 75.8% alpha, 2.7% beta 108 base pairs and 192 stacking pairs defined. Time for finding SS restraints: 4.49 Creating SS restraints... Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.541A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.546A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.844A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.034A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.666A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 4.139A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.559A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.382A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.532A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.740A 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 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.772A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.560A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.860A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.625A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.541A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 77 removed outlier: 4.299A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.619A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.311A 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 'C' and resid 42 through 43 removed outlier: 7.380A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.406A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.762A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 278 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 281 hydrogen bonds 562 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 192 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 4.85 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: 1737 1.33 - 1.45: 3088 1.45 - 1.57: 4005 1.57 - 1.69: 436 1.69 - 1.81: 16 Bond restraints: 9282 Sorted by residual: bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.56e+00 bond pdb=" CG GLU C 61 " pdb=" CD GLU C 61 " ideal model delta sigma weight residual 1.516 1.463 0.053 2.50e-02 1.60e+03 4.52e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.41e+00 bond pdb=" C ALA C 60 " pdb=" N GLU C 61 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.31e-02 5.83e+03 2.41e+00 bond pdb=" N GLU C 61 " pdb=" CA GLU C 61 " ideal model delta sigma weight residual 1.459 1.478 -0.019 1.21e-02 6.83e+03 2.40e+00 ... (remaining 9277 not shown) Histogram of bond angle deviations from ideal: 98.22 - 105.22: 988 105.22 - 112.22: 5012 112.22 - 119.22: 2780 119.22 - 126.22: 4012 126.22 - 133.22: 685 Bond angle restraints: 13477 Sorted by residual: angle pdb=" N GLU C 61 " pdb=" CA GLU C 61 " pdb=" CB GLU C 61 " ideal model delta sigma weight residual 110.12 118.88 -8.76 1.47e+00 4.63e-01 3.55e+01 angle pdb=" CB MET D 56 " pdb=" CG MET D 56 " pdb=" SD MET D 56 " ideal model delta sigma weight residual 112.70 127.20 -14.50 3.00e+00 1.11e-01 2.34e+01 angle pdb=" CA GLU C 61 " pdb=" CB GLU C 61 " pdb=" CG GLU C 61 " ideal model delta sigma weight residual 114.10 123.44 -9.34 2.00e+00 2.50e-01 2.18e+01 angle pdb=" CA LEU C 115 " pdb=" CB LEU C 115 " pdb=" CG LEU C 115 " ideal model delta sigma weight residual 116.30 129.46 -13.16 3.50e+00 8.16e-02 1.41e+01 angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 122.46 127.63 -5.17 1.41e+00 5.03e-01 1.34e+01 ... (remaining 13472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 3935 35.02 - 70.04: 1052 70.04 - 105.07: 14 105.07 - 140.09: 0 140.09 - 175.11: 2 Dihedral angle restraints: 5003 sinusoidal: 3480 harmonic: 1523 Sorted by residual: dihedral pdb=" CA LYS F 77 " pdb=" C LYS F 77 " pdb=" N ARG F 78 " pdb=" CA ARG F 78 " ideal model delta harmonic sigma weight residual 180.00 155.89 24.11 0 5.00e+00 4.00e-02 2.32e+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 -159.80 -20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 35.11 -175.11 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 5000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1336 0.071 - 0.142: 184 0.142 - 0.213: 12 0.213 - 0.284: 3 0.284 - 0.354: 1 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CG LEU E 61 " pdb=" CB LEU E 61 " pdb=" CD1 LEU E 61 " pdb=" CD2 LEU E 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" P DG J 21 " pdb=" OP1 DG J 21 " pdb=" OP2 DG J 21 " pdb=" O5' DG J 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.56 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1533 not shown) Planarity restraints: 944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.055 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO C 80 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -54 " -0.032 2.00e-02 2.50e+03 1.46e-02 5.84e+00 pdb=" N9 DA I -54 " 0.033 2.00e-02 2.50e+03 pdb=" C8 DA I -54 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I -54 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DA I -54 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA I -54 " -0.006 2.00e-02 2.50e+03 pdb=" N6 DA I -54 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -54 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I -54 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -54 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -54 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 80 " -0.023 2.00e-02 2.50e+03 1.69e-02 5.74e+00 pdb=" CG TYR D 80 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR D 80 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 80 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR D 80 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR D 80 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR D 80 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 80 " 0.001 2.00e-02 2.50e+03 ... (remaining 941 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2066 2.82 - 3.34: 7286 3.34 - 3.86: 17089 3.86 - 4.38: 19200 4.38 - 4.90: 26702 Nonbonded interactions: 72343 Sorted by model distance: nonbonded pdb=" OH TYR D 37 " pdb=" OP1 DG J 48 " model vdw 2.305 2.440 nonbonded pdb=" OG1 THR B 30 " pdb=" OP1 DC I -12 " model vdw 2.324 2.440 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.329 2.440 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.346 2.440 nonbonded pdb=" ND2 ASN E 108 " pdb=" O GLY F 42 " model vdw 2.366 2.520 ... (remaining 72338 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 'B' and resid 24 through 94) selection = (chain 'F' and resid 24 through 94) } 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: 6.880 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: 21.700 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 31.710 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 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 0.066 9282 Z= 0.335 Angle : 0.874 14.501 13477 Z= 0.496 Chirality : 0.050 0.354 1536 Planarity : 0.008 0.083 944 Dihedral : 28.214 175.111 4017 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -0.99 (0.33), residues: 512 helix: -0.35 (0.24), residues: 373 sheet: None (None), residues: 0 loop : -1.14 (0.45), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 113 PHE 0.016 0.003 PHE E 84 TYR 0.039 0.004 TYR D 80 ARG 0.015 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3466 time to fit residues: 93.3925 Evaluate side-chains 218 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.679 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 9282 Z= 0.315 Angle : 0.662 11.329 13477 Z= 0.391 Chirality : 0.037 0.190 1536 Planarity : 0.005 0.064 944 Dihedral : 30.918 176.476 2968 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.12 % Allowed : 19.45 % Favored : 76.43 % 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: 1.00 (0.36), residues: 512 helix: 1.25 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.84 (0.47), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.015 0.002 PHE D 67 TYR 0.047 0.003 TYR F 88 ARG 0.007 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 230 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 16 residues processed: 231 average time/residue: 0.3534 time to fit residues: 98.9633 Evaluate side-chains 245 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 229 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0881 time to fit residues: 3.3347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9282 Z= 0.309 Angle : 0.647 11.356 13477 Z= 0.384 Chirality : 0.037 0.185 1536 Planarity : 0.005 0.058 944 Dihedral : 30.873 175.521 2968 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.66 % Allowed : 23.34 % Favored : 73.00 % 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: 1.47 (0.36), residues: 512 helix: 1.60 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.73 (0.49), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.002 PHE F 61 TYR 0.049 0.003 TYR F 88 ARG 0.008 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 233 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 233 average time/residue: 0.3446 time to fit residues: 97.0337 Evaluate side-chains 240 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 229 time to evaluate : 0.636 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0929 time to fit residues: 2.5177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9282 Z= 0.293 Angle : 0.645 11.749 13477 Z= 0.380 Chirality : 0.037 0.175 1536 Planarity : 0.005 0.057 944 Dihedral : 30.838 175.263 2968 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.66 % Allowed : 27.23 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.37), residues: 512 helix: 1.83 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.62 (0.50), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.002 PHE E 78 TYR 0.051 0.003 TYR F 88 ARG 0.008 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 230 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 232 average time/residue: 0.3460 time to fit residues: 97.4073 Evaluate side-chains 240 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 229 time to evaluate : 0.656 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1222 time to fit residues: 2.8947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9282 Z= 0.236 Angle : 0.620 12.151 13477 Z= 0.366 Chirality : 0.035 0.153 1536 Planarity : 0.004 0.047 944 Dihedral : 30.786 175.170 2968 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.52 % Allowed : 29.29 % Favored : 68.19 % 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: 2.03 (0.37), residues: 512 helix: 2.00 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.46 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE F 61 TYR 0.051 0.003 TYR F 88 ARG 0.008 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 228 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 228 average time/residue: 0.3460 time to fit residues: 95.6700 Evaluate side-chains 233 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 226 time to evaluate : 0.659 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1550 time to fit residues: 2.3163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.0270 chunk 5 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9282 Z= 0.226 Angle : 0.615 12.436 13477 Z= 0.362 Chirality : 0.034 0.149 1536 Planarity : 0.004 0.043 944 Dihedral : 30.725 175.006 2968 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.58 % Allowed : 29.75 % Favored : 65.68 % 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: 2.13 (0.37), residues: 512 helix: 2.05 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.33 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 82 PHE 0.008 0.001 PHE A 67 TYR 0.044 0.003 TYR F 88 ARG 0.008 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 226 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 228 average time/residue: 0.3586 time to fit residues: 99.2192 Evaluate side-chains 235 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 225 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1483 time to fit residues: 2.9093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 31 optimal weight: 0.2980 chunk 27 optimal weight: 0.2980 chunk 40 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN C 82 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9282 Z= 0.234 Angle : 0.630 11.499 13477 Z= 0.369 Chirality : 0.035 0.170 1536 Planarity : 0.005 0.041 944 Dihedral : 30.684 174.973 2968 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.29 % Allowed : 32.04 % Favored : 65.68 % 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: 2.09 (0.37), residues: 512 helix: 2.01 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.33 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 82 PHE 0.008 0.001 PHE A 67 TYR 0.062 0.004 TYR D 80 ARG 0.009 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 225 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 226 average time/residue: 0.3488 time to fit residues: 96.1286 Evaluate side-chains 230 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 224 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1382 time to fit residues: 2.0905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN C 68 ASN C 73 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9282 Z= 0.287 Angle : 0.661 13.028 13477 Z= 0.384 Chirality : 0.037 0.209 1536 Planarity : 0.005 0.050 944 Dihedral : 30.705 175.079 2968 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.06 % Allowed : 33.87 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.37), residues: 512 helix: 1.84 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.41 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.002 PHE F 61 TYR 0.060 0.004 TYR D 80 ARG 0.008 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 224 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 224 average time/residue: 0.3583 time to fit residues: 97.5130 Evaluate side-chains 229 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 222 time to evaluate : 0.665 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0958 time to fit residues: 1.9185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN C 68 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9282 Z= 0.325 Angle : 0.690 12.713 13477 Z= 0.399 Chirality : 0.039 0.172 1536 Planarity : 0.005 0.085 944 Dihedral : 30.743 175.390 2968 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.83 % Allowed : 34.10 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.37), residues: 512 helix: 1.75 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.45 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.002 PHE F 61 TYR 0.057 0.004 TYR D 80 ARG 0.010 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 220 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 221 average time/residue: 0.3579 time to fit residues: 95.6695 Evaluate side-chains 223 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 219 time to evaluate : 0.672 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0835 time to fit residues: 1.4377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN C 68 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9282 Z= 0.226 Angle : 0.668 15.035 13477 Z= 0.383 Chirality : 0.035 0.162 1536 Planarity : 0.005 0.045 944 Dihedral : 30.709 175.357 2968 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.60 % Allowed : 34.32 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.37), residues: 512 helix: 1.92 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -0.31 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.007 0.001 PHE A 67 TYR 0.058 0.004 TYR D 80 ARG 0.012 0.000 ARG F 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 221 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 221 average time/residue: 0.3808 time to fit residues: 101.8847 Evaluate side-chains 223 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 221 time to evaluate : 0.703 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2260 time to fit residues: 1.4069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN C 68 ASN C 73 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.132998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.109378 restraints weight = 16613.365| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.92 r_work: 0.3519 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9282 Z= 0.255 Angle : 0.682 14.323 13477 Z= 0.391 Chirality : 0.036 0.172 1536 Planarity : 0.007 0.143 944 Dihedral : 30.711 175.353 2968 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.60 % Allowed : 35.01 % Favored : 63.39 % 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: 1.83 (0.37), residues: 512 helix: 1.83 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -0.40 (0.51), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 46 PHE 0.021 0.002 PHE D 67 TYR 0.059 0.003 TYR D 80 ARG 0.015 0.001 ARG E 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2596.15 seconds wall clock time: 47 minutes 27.37 seconds (2847.37 seconds total)