Starting phenix.real_space_refine on Sat Jul 20 23:52:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/07_2024/8peo_17633.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/07_2024/8peo_17633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/07_2024/8peo_17633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/07_2024/8peo_17633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/07_2024/8peo_17633.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/07_2024/8peo_17633.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 294 5.49 5 S 13 5.16 5 C 7171 2.51 5 N 2399 2.21 5 O 2958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12835 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M2L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 9.32, per 1000 atoms: 0.73 Number of scatterers: 12835 At special positions: 0 Unit cell: (91.696, 119.205, 138.378, 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 13 16.00 P 294 15.00 O 2958 8.00 N 2399 7.00 C 7171 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.75 Conformation dependent library (CDL) restraints added in 1.3 seconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 64.5% alpha, 4.8% beta 146 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 6.44 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.569A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.613A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.858A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.569A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.807A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.575A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.801A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.508A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.794A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.602A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (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 45 through 72 removed outlier: 4.397A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 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 101 through 121 removed outlier: 4.112A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.720A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.477A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.143A 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 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.343A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.210A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 49 through 53 removed outlier: 3.839A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 4.80 Time building geometry restraints manager: 7.13 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: 2228 1.33 - 1.45: 4599 1.45 - 1.57: 6234 1.57 - 1.69: 586 1.69 - 1.82: 26 Bond restraints: 13673 Sorted by residual: bond pdb=" N ARG E 129 " pdb=" CA ARG E 129 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.20e-02 6.94e+03 5.59e+00 bond pdb=" N ASP E 123 " pdb=" CA ASP E 123 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.49e+00 bond pdb=" C TRP K 21 " pdb=" N PRO K 22 " ideal model delta sigma weight residual 1.332 1.358 -0.026 1.12e-02 7.97e+03 5.43e+00 bond pdb=" N ARG B 36 " pdb=" CA ARG B 36 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 5.09e+00 bond pdb=" P DG I -49 " pdb=" OP1 DG I -49 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.22e+00 ... (remaining 13668 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.26: 1321 105.26 - 112.43: 7523 112.43 - 119.60: 4514 119.60 - 126.77: 5533 126.77 - 133.94: 830 Bond angle restraints: 19721 Sorted by residual: angle pdb=" C ILE B 34 " pdb=" N ARG B 35 " pdb=" CA ARG B 35 " ideal model delta sigma weight residual 120.29 114.32 5.97 1.42e+00 4.96e-01 1.77e+01 angle pdb=" CA ASN G 73 " pdb=" CB ASN G 73 " pdb=" CG ASN G 73 " ideal model delta sigma weight residual 112.60 116.80 -4.20 1.00e+00 1.00e+00 1.77e+01 angle pdb=" CA ASN C 73 " pdb=" CB ASN C 73 " pdb=" CG ASN C 73 " ideal model delta sigma weight residual 112.60 116.63 -4.03 1.00e+00 1.00e+00 1.62e+01 angle pdb=" CA GLU D 68 " pdb=" CB GLU D 68 " pdb=" CG GLU D 68 " ideal model delta sigma weight residual 114.10 121.58 -7.48 2.00e+00 2.50e-01 1.40e+01 angle pdb=" C ASN G 73 " pdb=" CA ASN G 73 " pdb=" CB ASN G 73 " ideal model delta sigma weight residual 110.56 116.29 -5.73 1.69e+00 3.50e-01 1.15e+01 ... (remaining 19716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 5770 35.44 - 70.87: 1661 70.87 - 106.31: 37 106.31 - 141.74: 3 141.74 - 177.18: 4 Dihedral angle restraints: 7475 sinusoidal: 5003 harmonic: 2472 Sorted by residual: dihedral pdb=" CD M2L A 201 " pdb=" CE M2L A 201 " pdb=" NZ M2L A 201 " pdb=" CM1 M2L A 201 " ideal model delta sinusoidal sigma weight residual 66.23 -97.71 163.94 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C4' DT J 69 " pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sinusoidal sigma weight residual 220.00 42.82 177.18 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 68 " pdb=" C3' DC J 68 " pdb=" O3' DC J 68 " pdb=" P DT J 69 " ideal model delta sinusoidal sigma weight residual -140.00 24.39 -164.39 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 7472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2154 0.104 - 0.208: 70 0.208 - 0.313: 1 0.313 - 0.417: 0 0.417 - 0.521: 4 Chirality restraints: 2229 Sorted by residual: chirality pdb=" P DG J 50 " pdb=" OP1 DG J 50 " pdb=" OP2 DG J 50 " pdb=" O5' DG J 50 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.78e+00 chirality pdb=" P DC J 49 " pdb=" OP1 DC J 49 " pdb=" OP2 DC J 49 " pdb=" O5' DC J 49 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.52 2.00e-01 2.50e+01 6.67e+00 chirality pdb=" P DC I -50 " pdb=" OP1 DC I -50 " pdb=" OP2 DC I -50 " pdb=" O5' DC I -50 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.52 2.00e-01 2.50e+01 6.65e+00 ... (remaining 2226 not shown) Planarity restraints: 1477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 73 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C ASN G 73 " 0.067 2.00e-02 2.50e+03 pdb=" O ASN G 73 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS G 74 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 69 " -0.040 2.00e-02 2.50e+03 2.41e-02 1.31e+01 pdb=" N1 DC I 69 " 0.057 2.00e-02 2.50e+03 pdb=" C2 DC I 69 " -0.013 2.00e-02 2.50e+03 pdb=" O2 DC I 69 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I 69 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 69 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 69 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DC I 69 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DC I 69 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 49 " 0.030 2.00e-02 2.50e+03 2.39e-02 1.28e+01 pdb=" N1 DC I 49 " -0.057 2.00e-02 2.50e+03 pdb=" C2 DC I 49 " 0.028 2.00e-02 2.50e+03 pdb=" O2 DC I 49 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC I 49 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 49 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 49 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DC I 49 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DC I 49 " -0.001 2.00e-02 2.50e+03 ... (remaining 1474 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1279 2.74 - 3.28: 10720 3.28 - 3.82: 25198 3.82 - 4.36: 30038 4.36 - 4.90: 43095 Nonbonded interactions: 110330 Sorted by model distance: nonbonded pdb=" O GLU K 66 " pdb=" NZ LYS K 70 " model vdw 2.201 2.520 nonbonded pdb=" N GLU A 59 " pdb=" OE1 GLU A 59 " model vdw 2.204 2.520 nonbonded pdb=" NZ LYS H 43 " pdb=" O THR H 49 " model vdw 2.219 2.520 nonbonded pdb=" O TRP K 82 " pdb=" ND2 ASN K 86 " model vdw 2.241 2.520 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.254 2.440 ... (remaining 110325 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 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 4.980 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 44.940 Find NCS groups from input model: 0.320 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: 0.000 Load rotamer database and sin/cos tables:10.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13673 Z= 0.296 Angle : 0.772 8.793 19721 Z= 0.458 Chirality : 0.051 0.521 2229 Planarity : 0.006 0.119 1477 Dihedral : 29.822 177.176 5877 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.14 % Allowed : 20.20 % Favored : 79.66 % 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 (0.29), residues: 831 helix: 1.68 (0.22), residues: 548 sheet: -2.59 (0.96), residues: 23 loop : -1.27 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP K 82 HIS 0.007 0.001 HIS C 82 PHE 0.014 0.002 PHE K 5 TYR 0.013 0.002 TYR F 51 ARG 0.014 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 1.9035 time to fit residues: 335.8237 Evaluate side-chains 113 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN ** K 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13673 Z= 0.198 Angle : 0.591 10.700 19721 Z= 0.351 Chirality : 0.035 0.135 2229 Planarity : 0.004 0.042 1477 Dihedral : 31.100 178.349 4163 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.10 % Allowed : 21.46 % Favored : 76.44 % 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 (0.29), residues: 831 helix: 2.33 (0.22), residues: 562 sheet: -1.72 (1.12), residues: 21 loop : -0.89 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 21 HIS 0.004 0.001 HIS E 113 PHE 0.010 0.001 PHE K 5 TYR 0.008 0.001 TYR K 68 ARG 0.007 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: E 120 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8243 (mtt) outliers start: 15 outliers final: 4 residues processed: 134 average time/residue: 1.7520 time to fit residues: 249.6397 Evaluate side-chains 122 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN D 44 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13673 Z= 0.271 Angle : 0.601 10.488 19721 Z= 0.356 Chirality : 0.037 0.144 2229 Planarity : 0.004 0.040 1477 Dihedral : 31.095 176.922 4163 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.52 % Allowed : 20.20 % Favored : 77.28 % 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: 2.20 (0.29), residues: 831 helix: 2.46 (0.22), residues: 563 sheet: -1.52 (1.19), residues: 21 loop : -0.68 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 21 HIS 0.005 0.001 HIS D 106 PHE 0.008 0.001 PHE E 104 TYR 0.010 0.001 TYR F 51 ARG 0.006 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8299 (mtt) REVERT: G 73 ASN cc_start: 0.8588 (t0) cc_final: 0.8359 (t0) outliers start: 18 outliers final: 10 residues processed: 127 average time/residue: 1.7445 time to fit residues: 235.4229 Evaluate side-chains 129 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 90 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13673 Z= 0.210 Angle : 0.562 11.295 19721 Z= 0.335 Chirality : 0.034 0.132 2229 Planarity : 0.004 0.040 1477 Dihedral : 30.681 178.334 4163 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.10 % Allowed : 21.18 % Favored : 76.72 % 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 (0.29), residues: 831 helix: 2.67 (0.22), residues: 564 sheet: -1.80 (0.99), residues: 21 loop : -0.61 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 82 HIS 0.002 0.001 HIS B 75 PHE 0.007 0.001 PHE A 67 TYR 0.008 0.001 TYR K 61 ARG 0.006 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8270 (mtt) REVERT: G 73 ASN cc_start: 0.8604 (t0) cc_final: 0.8356 (t0) REVERT: K 83 GLU cc_start: 0.7905 (pt0) cc_final: 0.7682 (pt0) outliers start: 15 outliers final: 7 residues processed: 131 average time/residue: 1.7742 time to fit residues: 246.5579 Evaluate side-chains 124 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.1980 chunk 59 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13673 Z= 0.191 Angle : 0.569 11.087 19721 Z= 0.337 Chirality : 0.034 0.126 2229 Planarity : 0.004 0.040 1477 Dihedral : 30.652 178.342 4163 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.68 % Allowed : 21.04 % Favored : 77.28 % 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: 2.60 (0.29), residues: 831 helix: 2.78 (0.22), residues: 564 sheet: -1.93 (0.86), residues: 23 loop : -0.51 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 82 HIS 0.002 0.001 HIS F 18 PHE 0.007 0.001 PHE A 67 TYR 0.010 0.001 TYR F 51 ARG 0.007 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 97 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8377 (mp0) REVERT: E 120 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8267 (mtt) REVERT: G 73 ASN cc_start: 0.8625 (t0) cc_final: 0.8361 (t0) outliers start: 12 outliers final: 7 residues processed: 126 average time/residue: 1.7839 time to fit residues: 238.8341 Evaluate side-chains 126 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13673 Z= 0.205 Angle : 0.560 10.754 19721 Z= 0.333 Chirality : 0.034 0.125 2229 Planarity : 0.003 0.040 1477 Dihedral : 30.510 178.843 4163 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.24 % Allowed : 21.32 % Favored : 76.44 % 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: 2.69 (0.29), residues: 831 helix: 2.84 (0.22), residues: 564 sheet: -1.99 (0.83), residues: 23 loop : -0.44 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 82 HIS 0.002 0.001 HIS B 75 PHE 0.007 0.001 PHE A 67 TYR 0.009 0.001 TYR F 51 ARG 0.004 0.000 ARG K 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8267 (mtt) REVERT: G 73 ASN cc_start: 0.8598 (t0) cc_final: 0.8377 (t0) outliers start: 16 outliers final: 9 residues processed: 132 average time/residue: 1.6943 time to fit residues: 237.9071 Evaluate side-chains 127 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN E 113 HIS G 104 GLN K 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13673 Z= 0.203 Angle : 0.563 10.985 19721 Z= 0.332 Chirality : 0.034 0.129 2229 Planarity : 0.003 0.040 1477 Dihedral : 30.411 179.025 4163 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.38 % Allowed : 20.76 % Favored : 76.86 % 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: 2.75 (0.29), residues: 831 helix: 2.87 (0.22), residues: 564 sheet: -1.86 (0.83), residues: 23 loop : -0.40 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 82 HIS 0.002 0.001 HIS B 75 PHE 0.007 0.001 PHE A 67 TYR 0.007 0.001 TYR K 68 ARG 0.004 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8276 (mtt) REVERT: G 73 ASN cc_start: 0.8619 (t0) cc_final: 0.8377 (t0) outliers start: 17 outliers final: 9 residues processed: 128 average time/residue: 1.6373 time to fit residues: 223.4990 Evaluate side-chains 128 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 25 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN F 18 HIS G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13673 Z= 0.223 Angle : 0.575 10.866 19721 Z= 0.338 Chirality : 0.034 0.132 2229 Planarity : 0.004 0.040 1477 Dihedral : 30.417 178.890 4163 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.38 % Allowed : 22.02 % Favored : 75.60 % 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: 2.72 (0.29), residues: 831 helix: 2.85 (0.22), residues: 564 sheet: -1.86 (0.87), residues: 23 loop : -0.39 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 82 HIS 0.003 0.001 HIS F 18 PHE 0.007 0.001 PHE K 5 TYR 0.008 0.001 TYR K 68 ARG 0.002 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8274 (mtt) REVERT: G 73 ASN cc_start: 0.8628 (t0) cc_final: 0.8379 (t0) outliers start: 17 outliers final: 11 residues processed: 128 average time/residue: 1.7145 time to fit residues: 233.5005 Evaluate side-chains 128 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN E 76 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 13673 Z= 0.412 Angle : 0.647 11.776 19721 Z= 0.376 Chirality : 0.041 0.143 2229 Planarity : 0.005 0.038 1477 Dihedral : 30.704 177.612 4163 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.82 % Allowed : 22.58 % Favored : 75.60 % 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: 2.33 (0.29), residues: 831 helix: 2.60 (0.21), residues: 557 sheet: -2.38 (0.88), residues: 26 loop : -0.50 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 82 HIS 0.007 0.001 HIS F 18 PHE 0.016 0.002 PHE K 5 TYR 0.011 0.002 TYR K 68 ARG 0.005 0.001 ARG G 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8386 (mtt) outliers start: 13 outliers final: 9 residues processed: 126 average time/residue: 1.7377 time to fit residues: 232.9455 Evaluate side-chains 125 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 63 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13673 Z= 0.213 Angle : 0.619 11.199 19721 Z= 0.362 Chirality : 0.036 0.145 2229 Planarity : 0.004 0.039 1477 Dihedral : 30.709 177.787 4163 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.54 % Allowed : 23.00 % Favored : 75.46 % 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: 2.40 (0.29), residues: 831 helix: 2.62 (0.22), residues: 557 sheet: -2.30 (0.90), residues: 26 loop : -0.40 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 21 HIS 0.005 0.001 HIS F 18 PHE 0.012 0.001 PHE K 5 TYR 0.012 0.001 TYR K 68 ARG 0.004 0.000 ARG K 3 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: E 120 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8327 (mtt) REVERT: G 73 ASN cc_start: 0.8655 (t0) cc_final: 0.8384 (t0) outliers start: 11 outliers final: 6 residues processed: 122 average time/residue: 1.7102 time to fit residues: 221.9672 Evaluate side-chains 121 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 25 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 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 76 GLN D 44 GLN E 76 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.072327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.049681 restraints weight = 35452.169| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.54 r_work: 0.2687 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13673 Z= 0.224 Angle : 0.609 11.088 19721 Z= 0.357 Chirality : 0.036 0.132 2229 Planarity : 0.004 0.040 1477 Dihedral : 30.633 177.764 4163 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.40 % Allowed : 23.00 % Favored : 75.60 % 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: 2.51 (0.29), residues: 831 helix: 2.70 (0.22), residues: 559 sheet: -2.23 (0.90), residues: 26 loop : -0.35 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 21 HIS 0.006 0.001 HIS F 18 PHE 0.010 0.001 PHE K 52 TYR 0.012 0.001 TYR K 68 ARG 0.006 0.000 ARG K 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4625.35 seconds wall clock time: 81 minutes 18.42 seconds (4878.42 seconds total)