Starting phenix.real_space_refine on Fri Mar 15 09:55:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl0_12453/03_2024/7nl0_12453.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl0_12453/03_2024/7nl0_12453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl0_12453/03_2024/7nl0_12453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl0_12453/03_2024/7nl0_12453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl0_12453/03_2024/7nl0_12453.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl0_12453/03_2024/7nl0_12453.pdb" } resolution = 3.5 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= 0.001 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 262 5.49 5 S 14 5.16 5 C 6334 2.51 5 N 2121 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H ARG 30": "NH1" <-> "NH2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11363 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" 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: "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: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2715 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "J" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2656 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Time building chain proxies: 6.23, per 1000 atoms: 0.55 Number of scatterers: 11363 At special positions: 0 Unit cell: (75.9676, 120.12, 116.873, 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 262 15.00 O 2632 8.00 N 2121 7.00 C 6334 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: 5.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 73.0% alpha, 2.4% beta 127 base pairs and 223 stacking pairs defined. Time for finding SS restraints: 5.28 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.820A 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 24 through 29 removed outlier: 3.671A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.802A 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 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.505A 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 92 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 53 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.591A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.500A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.787A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.638A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.727A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (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 removed outlier: 3.513A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.350A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.413A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.676A 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: 7.283A 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 77 through 78 409 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 307 hydrogen bonds 614 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 223 stacking parallelities Total time for adding SS restraints: 4.04 Time building geometry restraints manager: 5.73 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: 2176 1.33 - 1.45: 3809 1.45 - 1.57: 5564 1.57 - 1.69: 522 1.69 - 1.81: 24 Bond restraints: 12095 Sorted by residual: bond pdb=" C3' DA I 58 " pdb=" O3' DA I 58 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.88e+00 bond pdb=" CG1 ILE H 86 " pdb=" CD1 ILE H 86 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.94e+00 bond pdb=" C3' DA I 14 " pdb=" O3' DA I 14 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.81e+00 bond pdb=" CG1 ILE D 86 " pdb=" CD1 ILE D 86 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.49e+00 bond pdb=" C3' DC J -52 " pdb=" O3' DC J -52 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.78e+00 ... (remaining 12090 not shown) Histogram of bond angle deviations from ideal: 98.05 - 104.96: 1135 104.96 - 111.88: 6512 111.88 - 118.79: 3189 118.79 - 125.71: 5729 125.71 - 132.63: 886 Bond angle restraints: 17451 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.71 107.75 5.96 9.50e-01 1.11e+00 3.94e+01 angle pdb=" C GLY G 37 " pdb=" N ASN G 38 " pdb=" CA ASN G 38 " ideal model delta sigma weight residual 121.54 127.28 -5.74 1.91e+00 2.74e-01 9.04e+00 angle pdb=" CA VAL A 117 " pdb=" C VAL A 117 " pdb=" N THR A 118 " ideal model delta sigma weight residual 119.87 116.36 3.51 1.34e+00 5.57e-01 6.87e+00 angle pdb=" C3' DA I 58 " pdb=" O3' DA I 58 " pdb=" P DT I 59 " ideal model delta sigma weight residual 120.20 124.04 -3.84 1.50e+00 4.44e-01 6.54e+00 angle pdb=" C3' DA I 14 " pdb=" O3' DA I 14 " pdb=" P DA I 15 " ideal model delta sigma weight residual 120.20 123.98 -3.78 1.50e+00 4.44e-01 6.34e+00 ... (remaining 17446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 5243 35.14 - 70.28: 1400 70.28 - 105.43: 23 105.43 - 140.57: 3 140.57 - 175.71: 9 Dihedral angle restraints: 6678 sinusoidal: 4495 harmonic: 2183 Sorted by residual: dihedral pdb=" CA TYR G 39 " pdb=" C TYR G 39 " pdb=" N SER G 40 " pdb=" CA SER G 40 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" C4' DG J 30 " pdb=" C3' DG J 30 " pdb=" O3' DG J 30 " pdb=" P DA J 31 " ideal model delta sinusoidal sigma weight residual -140.00 35.71 -175.71 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " pdb=" P DG I -16 " ideal model delta sinusoidal sigma weight residual -140.00 33.83 -173.83 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1249 0.032 - 0.065: 536 0.065 - 0.097: 147 0.097 - 0.129: 47 0.129 - 0.161: 4 Chirality restraints: 1983 Sorted by residual: chirality pdb=" CA ASN G 38 " pdb=" N ASN G 38 " pdb=" C ASN G 38 " pdb=" CB ASN G 38 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" P DT I 59 " pdb=" OP1 DT I 59 " pdb=" OP2 DT I 59 " pdb=" O5' DT I 59 " both_signs ideal model delta sigma weight residual True 2.35 -2.48 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA VAL C 107 " pdb=" N VAL C 107 " pdb=" C VAL C 107 " pdb=" CB VAL C 107 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 1980 not shown) Planarity restraints: 1305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -24 " -0.027 2.00e-02 2.50e+03 1.18e-02 3.80e+00 pdb=" N9 DA I -24 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DA I -24 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I -24 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DA I -24 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -24 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I -24 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -24 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -24 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I -24 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -24 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 16 " 0.027 2.00e-02 2.50e+03 1.10e-02 3.66e+00 pdb=" N9 DG I 16 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DG I 16 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 16 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DG I 16 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DG I 16 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG I 16 " 0.013 2.00e-02 2.50e+03 pdb=" N1 DG I 16 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG I 16 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DG I 16 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 16 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 16 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " 0.025 2.00e-02 2.50e+03 1.08e-02 3.50e+00 pdb=" N9 DG I 28 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " -0.002 2.00e-02 2.50e+03 ... (remaining 1302 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 559 2.70 - 3.25: 9965 3.25 - 3.80: 22342 3.80 - 4.35: 27582 4.35 - 4.90: 39438 Nonbonded interactions: 99886 Sorted by model distance: nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.147 2.440 nonbonded pdb=" OD1 ASP C 90 " pdb=" N GLU C 91 " model vdw 2.185 2.520 nonbonded pdb=" NE ARG A 131 " pdb=" OE2 GLU A 133 " model vdw 2.233 2.520 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.237 2.440 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.251 2.520 ... (remaining 99881 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 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 13 through 117) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 10.900 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 36.060 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 0.067 12095 Z= 0.368 Angle : 0.709 8.036 17451 Z= 0.428 Chirality : 0.039 0.161 1983 Planarity : 0.004 0.040 1305 Dihedral : 29.742 175.712 5272 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 0.67 (0.30), residues: 739 helix: 1.29 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -1.90 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 79 PHE 0.024 0.003 PHE C 25 TYR 0.012 0.002 TYR F 51 ARG 0.005 0.000 ARG G 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.894 Fit side-chains REVERT: E 59 GLU cc_start: 0.7178 (pp20) cc_final: 0.6897 (pm20) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.3466 time to fit residues: 58.7244 Evaluate side-chains 121 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.0522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12095 Z= 0.239 Angle : 0.646 8.895 17451 Z= 0.379 Chirality : 0.037 0.158 1983 Planarity : 0.004 0.035 1305 Dihedral : 32.924 176.473 3777 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.75 % Allowed : 7.02 % Favored : 91.23 % 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: 1.26 (0.31), residues: 739 helix: 1.73 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.80 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 31 PHE 0.010 0.002 PHE A 67 TYR 0.012 0.002 TYR C 57 ARG 0.004 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 0.850 Fit side-chains REVERT: E 59 GLU cc_start: 0.7225 (pp20) cc_final: 0.6948 (pm20) REVERT: G 41 GLU cc_start: 0.7405 (pp20) cc_final: 0.7181 (pp20) outliers start: 11 outliers final: 11 residues processed: 131 average time/residue: 0.3214 time to fit residues: 54.2954 Evaluate side-chains 134 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12095 Z= 0.335 Angle : 0.666 7.162 17451 Z= 0.386 Chirality : 0.038 0.158 1983 Planarity : 0.004 0.036 1305 Dihedral : 32.877 177.763 3777 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.07 % Allowed : 9.57 % Favored : 88.36 % 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: 1.39 (0.31), residues: 739 helix: 1.85 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.84 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 31 PHE 0.014 0.003 PHE E 67 TYR 0.013 0.002 TYR C 57 ARG 0.008 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.901 Fit side-chains REVERT: E 59 GLU cc_start: 0.7209 (pp20) cc_final: 0.7001 (pm20) REVERT: G 41 GLU cc_start: 0.7450 (pp20) cc_final: 0.7186 (pp20) outliers start: 13 outliers final: 11 residues processed: 125 average time/residue: 0.3241 time to fit residues: 52.7983 Evaluate side-chains 131 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 38 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12095 Z= 0.209 Angle : 0.618 7.194 17451 Z= 0.366 Chirality : 0.036 0.162 1983 Planarity : 0.004 0.039 1305 Dihedral : 32.879 178.198 3777 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.55 % Allowed : 11.16 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.31), residues: 739 helix: 2.08 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.76 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 31 PHE 0.013 0.002 PHE A 67 TYR 0.016 0.001 TYR C 57 ARG 0.007 0.000 ARG D 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.833 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 133 average time/residue: 0.3127 time to fit residues: 54.3857 Evaluate side-chains 136 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.0970 chunk 38 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12095 Z= 0.188 Angle : 0.599 6.311 17451 Z= 0.357 Chirality : 0.035 0.141 1983 Planarity : 0.004 0.042 1305 Dihedral : 32.787 179.424 3777 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.91 % Allowed : 11.80 % Favored : 86.28 % 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: 1.96 (0.31), residues: 739 helix: 2.26 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.68 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 31 PHE 0.014 0.002 PHE A 67 TYR 0.027 0.002 TYR C 39 ARG 0.003 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.893 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 129 average time/residue: 0.3136 time to fit residues: 53.2438 Evaluate side-chains 131 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.0770 chunk 84 optimal weight: 10.0000 chunk 18 optimal weight: 0.0470 chunk 55 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12095 Z= 0.179 Angle : 0.593 8.551 17451 Z= 0.353 Chirality : 0.035 0.140 1983 Planarity : 0.004 0.042 1305 Dihedral : 32.723 179.938 3777 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.44 % Allowed : 13.08 % Favored : 85.49 % 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: 2.20 (0.31), residues: 739 helix: 2.43 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -1.62 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 31 PHE 0.014 0.002 PHE A 67 TYR 0.013 0.001 TYR C 57 ARG 0.004 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 0.791 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 134 average time/residue: 0.3228 time to fit residues: 56.5987 Evaluate side-chains 134 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 79 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12095 Z= 0.198 Angle : 0.590 5.936 17451 Z= 0.351 Chirality : 0.035 0.141 1983 Planarity : 0.004 0.041 1305 Dihedral : 32.677 179.799 3777 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.23 % Allowed : 13.24 % Favored : 84.53 % 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: 2.30 (0.31), residues: 739 helix: 2.49 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -1.55 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 31 PHE 0.018 0.002 PHE D 62 TYR 0.017 0.001 TYR C 57 ARG 0.002 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.933 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 132 average time/residue: 0.3075 time to fit residues: 53.2748 Evaluate side-chains 131 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.0040 chunk 73 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12095 Z= 0.217 Angle : 0.594 5.959 17451 Z= 0.353 Chirality : 0.035 0.146 1983 Planarity : 0.004 0.041 1305 Dihedral : 32.666 179.697 3777 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.71 % Allowed : 13.72 % Favored : 83.57 % 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: 2.26 (0.30), residues: 739 helix: 2.47 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -1.54 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 31 PHE 0.012 0.002 PHE D 62 TYR 0.015 0.001 TYR C 57 ARG 0.003 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 0.819 Fit side-chains REVERT: H 69 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.8067 (mtm180) outliers start: 17 outliers final: 13 residues processed: 131 average time/residue: 0.3214 time to fit residues: 55.1315 Evaluate side-chains 134 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 12095 Z= 0.359 Angle : 0.660 8.289 17451 Z= 0.383 Chirality : 0.038 0.164 1983 Planarity : 0.004 0.036 1305 Dihedral : 32.815 178.707 3777 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.55 % Allowed : 14.19 % Favored : 83.25 % 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: 1.81 (0.30), residues: 739 helix: 2.08 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -1.54 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS G 31 PHE 0.016 0.003 PHE G 25 TYR 0.017 0.002 TYR C 57 ARG 0.004 0.000 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.883 Fit side-chains REVERT: B 79 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7864 (mtmm) REVERT: H 69 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.8153 (mtm180) outliers start: 16 outliers final: 14 residues processed: 130 average time/residue: 0.3220 time to fit residues: 54.5395 Evaluate side-chains 137 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 61 optimal weight: 0.0270 chunk 81 optimal weight: 5.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12095 Z= 0.185 Angle : 0.580 7.641 17451 Z= 0.345 Chirality : 0.035 0.145 1983 Planarity : 0.004 0.044 1305 Dihedral : 32.444 178.141 3777 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.23 % Allowed : 14.35 % Favored : 83.41 % 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: 2.36 (0.31), residues: 739 helix: 2.52 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -1.49 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 31 PHE 0.015 0.002 PHE A 67 TYR 0.016 0.001 TYR C 57 ARG 0.004 0.000 ARG H 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 0.891 Fit side-chains REVERT: B 79 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7806 (mtmm) REVERT: D 56 MET cc_start: 0.8172 (tpt) cc_final: 0.7915 (tpt) REVERT: E 56 LYS cc_start: 0.7538 (ttmm) cc_final: 0.7259 (mtmt) REVERT: H 69 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.8116 (mtm180) outliers start: 14 outliers final: 12 residues processed: 135 average time/residue: 0.3235 time to fit residues: 57.1977 Evaluate side-chains 139 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.143296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105219 restraints weight = 18583.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.107351 restraints weight = 12442.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.108654 restraints weight = 10079.068| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12095 Z= 0.204 Angle : 0.583 8.009 17451 Z= 0.345 Chirality : 0.035 0.146 1983 Planarity : 0.004 0.043 1305 Dihedral : 32.420 177.607 3777 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.91 % Allowed : 14.99 % Favored : 83.09 % 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: 2.45 (0.31), residues: 739 helix: 2.59 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -1.42 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 31 PHE 0.012 0.002 PHE A 67 TYR 0.016 0.001 TYR C 57 ARG 0.004 0.000 ARG H 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1948.26 seconds wall clock time: 35 minutes 57.36 seconds (2157.36 seconds total)