Starting phenix.real_space_refine on Wed Jun 11 02:47:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dg3_46822/06_2025/9dg3_46822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dg3_46822/06_2025/9dg3_46822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dg3_46822/06_2025/9dg3_46822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dg3_46822/06_2025/9dg3_46822.map" model { file = "/net/cci-nas-00/data/ceres_data/9dg3_46822/06_2025/9dg3_46822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dg3_46822/06_2025/9dg3_46822.cif" } resolution = 3.46 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= 0.008 sd= 0.048 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 292 5.49 5 S 17 5.16 5 C 6967 2.51 5 N 2342 2.21 5 O 2934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12553 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 773 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3015 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2971 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "M" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 249 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 32} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "N" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 405 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 3, 'TRANS': 68} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11931 SG CYS M 27 29.583 48.634 68.684 1.00205.57 S ATOM 11950 SG CYS M 30 27.941 45.395 67.355 1.00208.97 S ATOM 12028 SG CYS M 41 29.688 45.285 70.695 1.00205.36 S ATOM 12048 SG CYS M 44 31.653 45.682 67.608 1.00195.86 S Time building chain proxies: 7.31, per 1000 atoms: 0.58 Number of scatterers: 12553 At special positions: 0 Unit cell: (103.024, 118.368, 122.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 17 16.00 P 292 15.00 O 2934 8.00 N 2342 7.00 C 6967 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 - 3.00 Amino acid : True - 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: 3.21 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 301 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 44 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 30 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 41 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 27 " Number of angles added : 6 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1616 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 65.6% alpha, 4.2% beta 143 base pairs and 253 stacking pairs defined. Time for finding SS restraints: 6.33 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.103A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (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 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 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 89 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 120 Processing helix chain 'E' and resid 44 through 56 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: 3.620A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.313A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 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 100 through 121 removed outlier: 3.583A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 35 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.810A 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: 7.472A 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 'E' and resid 83 through 84 removed outlier: 6.684A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.470A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'M' and resid 25 through 26 Processing sheet with id=AB2, first strand: chain 'N' and resid 12 through 16 436 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 726 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 253 stacking parallelities Total time for adding SS restraints: 4.39 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2848 1.34 - 1.46: 4190 1.46 - 1.58: 5715 1.58 - 1.70: 582 1.70 - 1.82: 27 Bond restraints: 13362 Sorted by residual: bond pdb=" C PHE E 84 " pdb=" N GLN E 85 " ideal model delta sigma weight residual 1.330 1.377 -0.047 1.38e-02 5.25e+03 1.17e+01 bond pdb=" N ILE D 51 " pdb=" CA ILE D 51 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N ASN C 73 " pdb=" CA ASN C 73 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.12e-02 7.97e+03 9.60e+00 bond pdb=" N VAL B 57 " pdb=" CA VAL B 57 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.19e+00 bond pdb=" N VAL B 21 " pdb=" CA VAL B 21 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 9.16e+00 ... (remaining 13357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 18804 2.15 - 4.30: 451 4.30 - 6.45: 57 6.45 - 8.60: 13 8.60 - 10.75: 4 Bond angle restraints: 19329 Sorted by residual: angle pdb=" N GLN B 27 " pdb=" CA GLN B 27 " pdb=" C GLN B 27 " ideal model delta sigma weight residual 114.16 103.58 10.58 1.48e+00 4.57e-01 5.11e+01 angle pdb=" CB LYS G 36 " pdb=" CG LYS G 36 " pdb=" CD LYS G 36 " ideal model delta sigma weight residual 111.30 122.05 -10.75 2.30e+00 1.89e-01 2.19e+01 angle pdb=" CB LYS G 13 " pdb=" CG LYS G 13 " pdb=" CD LYS G 13 " ideal model delta sigma weight residual 111.30 121.28 -9.98 2.30e+00 1.89e-01 1.88e+01 angle pdb=" N ASN C 73 " pdb=" CA ASN C 73 " pdb=" C ASN C 73 " ideal model delta sigma weight residual 112.97 108.61 4.36 1.06e+00 8.90e-01 1.69e+01 angle pdb=" CA ARG G 99 " pdb=" CB ARG G 99 " pdb=" CG ARG G 99 " ideal model delta sigma weight residual 114.10 122.21 -8.11 2.00e+00 2.50e-01 1.64e+01 ... (remaining 19324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.16: 5268 26.16 - 52.32: 1606 52.32 - 78.48: 382 78.48 - 104.64: 10 104.64 - 130.79: 2 Dihedral angle restraints: 7268 sinusoidal: 4772 harmonic: 2496 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 158.85 21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ILE B 26 " pdb=" C ILE B 26 " pdb=" N GLN B 27 " pdb=" CA GLN B 27 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C4' DC I 128 " pdb=" C3' DC I 128 " pdb=" O3' DC I 128 " pdb=" P DT I 129 " ideal model delta sinusoidal sigma weight residual 220.00 89.21 130.79 1 3.50e+01 8.16e-04 1.30e+01 ... (remaining 7265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2169 0.108 - 0.216: 57 0.216 - 0.324: 0 0.324 - 0.431: 0 0.431 - 0.539: 3 Chirality restraints: 2229 Sorted by residual: chirality pdb=" P DA J 151 " pdb=" OP1 DA J 151 " pdb=" OP2 DA J 151 " pdb=" O5' DA J 151 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" P DG J 152 " pdb=" OP1 DG J 152 " pdb=" OP2 DG J 152 " pdb=" O5' DG J 152 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" P DA J 153 " pdb=" OP1 DA J 153 " pdb=" OP2 DA J 153 " pdb=" O5' DA J 153 " both_signs ideal model delta sigma weight residual True 2.35 -2.85 -0.50 2.00e-01 2.50e+01 6.29e+00 ... (remaining 2226 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " -0.036 2.00e-02 2.50e+03 2.27e-02 1.03e+01 pdb=" CG TYR B 88 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 71 " 0.271 9.50e-02 1.11e+02 1.21e-01 9.07e+00 pdb=" NE ARG C 71 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 71 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 71 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 71 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 80 " -0.022 2.00e-02 2.50e+03 2.08e-02 8.65e+00 pdb=" CG TYR H 80 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR H 80 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR H 80 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR H 80 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR H 80 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR H 80 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR H 80 " -0.009 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 902 2.73 - 3.27: 11782 3.27 - 3.81: 25710 3.81 - 4.36: 28992 4.36 - 4.90: 41823 Nonbonded interactions: 109209 Sorted by model distance: nonbonded pdb=" O LEU G 85 " pdb=" OD1 ASN G 89 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 68 " model vdw 2.220 3.040 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 75 " model vdw 2.250 3.040 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 75 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR G 39 " pdb=" OE1 GLU H 68 " model vdw 2.288 3.040 ... (remaining 109204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 40 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 134)) } ncs_group { reference = (chain 'B' and resid 23 through 101) selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 117)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 117)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 37.220 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 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 0.054 13366 Z= 0.256 Angle : 0.791 10.752 19335 Z= 0.474 Chirality : 0.046 0.539 2229 Planarity : 0.007 0.121 1440 Dihedral : 28.102 130.794 5652 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.15 % Allowed : 22.19 % Favored : 77.66 % 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: 1.39 (0.28), residues: 840 helix: 1.54 (0.22), residues: 555 sheet: 1.21 (1.10), residues: 25 loop : -0.35 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP M 25 HIS 0.008 0.001 HIS H 46 PHE 0.012 0.002 PHE B 100 TYR 0.052 0.003 TYR B 88 ARG 0.007 0.001 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.06810 ( 803) hydrogen bonds : angle 4.12141 ( 2016) metal coordination : bond 0.01028 ( 4) metal coordination : angle 3.15875 ( 6) covalent geometry : bond 0.00491 (13362) covalent geometry : angle 0.78925 (19329) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: F 74 GLU cc_start: 0.9157 (tp30) cc_final: 0.8728 (tp30) REVERT: H 31 LYS cc_start: 0.8831 (ttpp) cc_final: 0.8516 (pttm) REVERT: H 65 ASP cc_start: 0.9228 (t0) cc_final: 0.9027 (t0) REVERT: H 80 TYR cc_start: 0.8323 (m-80) cc_final: 0.7947 (m-80) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.2913 time to fit residues: 71.7731 Evaluate side-chains 158 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.054546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.039863 restraints weight = 73313.155| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.94 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13366 Z= 0.194 Angle : 0.619 10.940 19335 Z= 0.364 Chirality : 0.036 0.161 2229 Planarity : 0.005 0.055 1440 Dihedral : 30.520 128.747 4132 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.13 % Allowed : 19.15 % Favored : 78.72 % 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: 1.71 (0.28), residues: 840 helix: 1.85 (0.22), residues: 558 sheet: 1.09 (1.09), residues: 25 loop : -0.41 (0.35), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP M 25 HIS 0.006 0.001 HIS B 75 PHE 0.008 0.001 PHE M 32 TYR 0.056 0.003 TYR B 88 ARG 0.006 0.001 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 803) hydrogen bonds : angle 3.54980 ( 2016) metal coordination : bond 0.01169 ( 4) metal coordination : angle 2.40884 ( 6) covalent geometry : bond 0.00424 (13362) covalent geometry : angle 0.61748 (19329) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8614 (tp30) cc_final: 0.8316 (tm-30) REVERT: C 92 GLU cc_start: 0.8109 (pm20) cc_final: 0.7721 (pm20) REVERT: D 65 ASP cc_start: 0.9057 (t0) cc_final: 0.8797 (t0) REVERT: F 53 GLU cc_start: 0.9361 (tp30) cc_final: 0.9012 (tp30) REVERT: H 31 LYS cc_start: 0.8843 (ttpp) cc_final: 0.8461 (pttm) REVERT: H 65 ASP cc_start: 0.9169 (t0) cc_final: 0.8924 (t0) REVERT: H 68 GLU cc_start: 0.9036 (tp30) cc_final: 0.8726 (tp30) REVERT: H 80 TYR cc_start: 0.8029 (m-10) cc_final: 0.7682 (m-80) outliers start: 14 outliers final: 9 residues processed: 174 average time/residue: 0.2735 time to fit residues: 66.3216 Evaluate side-chains 168 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain M residue 50 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.0770 chunk 86 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN E 68 GLN E 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.054243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.039599 restraints weight = 73246.765| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.89 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13366 Z= 0.180 Angle : 0.589 6.559 19335 Z= 0.349 Chirality : 0.035 0.178 2229 Planarity : 0.005 0.054 1440 Dihedral : 30.326 124.874 4132 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.98 % Allowed : 19.76 % Favored : 78.27 % 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: 1.98 (0.29), residues: 840 helix: 2.08 (0.22), residues: 560 sheet: 1.28 (1.13), residues: 25 loop : -0.40 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP M 25 HIS 0.005 0.001 HIS B 75 PHE 0.006 0.001 PHE E 78 TYR 0.018 0.002 TYR G 57 ARG 0.004 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 803) hydrogen bonds : angle 3.31973 ( 2016) metal coordination : bond 0.00868 ( 4) metal coordination : angle 2.45014 ( 6) covalent geometry : bond 0.00396 (13362) covalent geometry : angle 0.58782 (19329) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8604 (tt0) cc_final: 0.7840 (tm-30) REVERT: C 64 GLU cc_start: 0.8728 (tp30) cc_final: 0.8318 (tm-30) REVERT: C 90 ASP cc_start: 0.8314 (t0) cc_final: 0.7969 (t0) REVERT: D 43 LYS cc_start: 0.9332 (mmtm) cc_final: 0.8887 (tppt) REVERT: D 65 ASP cc_start: 0.9075 (t0) cc_final: 0.8829 (t0) REVERT: E 76 GLN cc_start: 0.8882 (mp10) cc_final: 0.8656 (mp10) REVERT: F 53 GLU cc_start: 0.9413 (tp30) cc_final: 0.9047 (tp30) REVERT: G 39 TYR cc_start: 0.8424 (m-80) cc_final: 0.8183 (m-80) REVERT: H 65 ASP cc_start: 0.9205 (t0) cc_final: 0.8959 (t0) REVERT: H 68 GLU cc_start: 0.9117 (tp30) cc_final: 0.8868 (tp30) REVERT: H 80 TYR cc_start: 0.8034 (m-10) cc_final: 0.7821 (m-80) outliers start: 13 outliers final: 7 residues processed: 179 average time/residue: 0.2965 time to fit residues: 73.3952 Evaluate side-chains 163 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 62 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 103 optimal weight: 30.0000 chunk 55 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.052957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.037491 restraints weight = 73553.572| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.99 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13366 Z= 0.198 Angle : 0.598 9.296 19335 Z= 0.351 Chirality : 0.035 0.207 2229 Planarity : 0.004 0.053 1440 Dihedral : 30.260 122.366 4132 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.74 % Allowed : 20.82 % 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: 2.12 (0.29), residues: 840 helix: 2.17 (0.22), residues: 564 sheet: 1.24 (1.16), residues: 25 loop : -0.36 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 25 HIS 0.006 0.001 HIS B 75 PHE 0.007 0.001 PHE B 61 TYR 0.016 0.002 TYR G 57 ARG 0.004 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.04701 ( 803) hydrogen bonds : angle 3.28985 ( 2016) metal coordination : bond 0.01067 ( 4) metal coordination : angle 2.55136 ( 6) covalent geometry : bond 0.00438 (13362) covalent geometry : angle 0.59611 (19329) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8515 (mtm) cc_final: 0.8141 (mtm) REVERT: B 59 LYS cc_start: 0.9284 (tmtt) cc_final: 0.9034 (tmtt) REVERT: C 64 GLU cc_start: 0.8742 (tp30) cc_final: 0.8438 (tm-30) REVERT: C 90 ASP cc_start: 0.8179 (t0) cc_final: 0.7730 (t0) REVERT: D 43 LYS cc_start: 0.9342 (mmtm) cc_final: 0.8931 (tppt) REVERT: D 65 ASP cc_start: 0.9110 (t0) cc_final: 0.8838 (t0) REVERT: D 85 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8820 (p) REVERT: D 90 GLU cc_start: 0.8393 (mp0) cc_final: 0.8192 (mp0) REVERT: E 76 GLN cc_start: 0.8807 (mp10) cc_final: 0.8520 (mp10) REVERT: G 92 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8095 (mt-10) REVERT: G 94 ASN cc_start: 0.9368 (OUTLIER) cc_final: 0.9013 (m-40) REVERT: H 65 ASP cc_start: 0.9257 (t0) cc_final: 0.9013 (t0) REVERT: H 68 GLU cc_start: 0.9086 (tp30) cc_final: 0.8801 (tp30) REVERT: H 80 TYR cc_start: 0.8136 (m-10) cc_final: 0.7795 (m-80) outliers start: 18 outliers final: 9 residues processed: 181 average time/residue: 0.2719 time to fit residues: 67.8050 Evaluate side-chains 169 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 5 optimal weight: 0.7980 chunk 64 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 104 optimal weight: 50.0000 chunk 103 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS H 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.053402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.038335 restraints weight = 72317.077| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.91 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13366 Z= 0.171 Angle : 0.588 7.496 19335 Z= 0.345 Chirality : 0.035 0.173 2229 Planarity : 0.004 0.052 1440 Dihedral : 30.271 120.729 4132 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.28 % Allowed : 22.64 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.29), residues: 840 helix: 2.21 (0.22), residues: 564 sheet: 1.25 (1.15), residues: 25 loop : -0.36 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 25 HIS 0.005 0.001 HIS B 75 PHE 0.006 0.001 PHE D 67 TYR 0.019 0.002 TYR G 57 ARG 0.004 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 803) hydrogen bonds : angle 3.20593 ( 2016) metal coordination : bond 0.00794 ( 4) metal coordination : angle 2.36683 ( 6) covalent geometry : bond 0.00375 (13362) covalent geometry : angle 0.58654 (19329) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8509 (mtm) cc_final: 0.8100 (mtm) REVERT: B 54 THR cc_start: 0.9539 (m) cc_final: 0.9250 (p) REVERT: B 59 LYS cc_start: 0.9281 (tmtt) cc_final: 0.8900 (tmtt) REVERT: C 64 GLU cc_start: 0.8729 (tp30) cc_final: 0.8425 (tm-30) REVERT: C 90 ASP cc_start: 0.8072 (t0) cc_final: 0.7819 (t0) REVERT: D 43 LYS cc_start: 0.9358 (mmtm) cc_final: 0.8993 (tppt) REVERT: D 65 ASP cc_start: 0.9129 (t0) cc_final: 0.8893 (t0) REVERT: E 76 GLN cc_start: 0.8732 (mp10) cc_final: 0.8398 (mp10) REVERT: G 94 ASN cc_start: 0.9240 (t0) cc_final: 0.9022 (t0) REVERT: H 65 ASP cc_start: 0.9210 (t0) cc_final: 0.8993 (t0) REVERT: H 68 GLU cc_start: 0.9157 (tp30) cc_final: 0.8929 (tp30) REVERT: H 80 TYR cc_start: 0.7956 (m-10) cc_final: 0.7680 (m-80) outliers start: 15 outliers final: 9 residues processed: 178 average time/residue: 0.2985 time to fit residues: 73.1807 Evaluate side-chains 171 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 46 HIS ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.052839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.037764 restraints weight = 73879.843| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.89 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13366 Z= 0.196 Angle : 0.593 7.704 19335 Z= 0.347 Chirality : 0.035 0.173 2229 Planarity : 0.004 0.050 1440 Dihedral : 30.275 119.902 4132 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.89 % Allowed : 23.25 % Favored : 73.86 % 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: 2.23 (0.29), residues: 840 helix: 2.27 (0.22), residues: 564 sheet: 2.44 (1.25), residues: 21 loop : -0.42 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 25 HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE B 61 TYR 0.034 0.002 TYR H 37 ARG 0.005 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 803) hydrogen bonds : angle 3.19329 ( 2016) metal coordination : bond 0.01061 ( 4) metal coordination : angle 2.55523 ( 6) covalent geometry : bond 0.00436 (13362) covalent geometry : angle 0.59112 (19329) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8539 (mtm) cc_final: 0.8125 (mtm) REVERT: B 54 THR cc_start: 0.9548 (m) cc_final: 0.9275 (p) REVERT: B 59 LYS cc_start: 0.9315 (tmtt) cc_final: 0.8930 (tmtt) REVERT: C 64 GLU cc_start: 0.8765 (tp30) cc_final: 0.8530 (tm-30) REVERT: C 90 ASP cc_start: 0.8037 (t0) cc_final: 0.7768 (t0) REVERT: D 43 LYS cc_start: 0.9348 (mmtm) cc_final: 0.8986 (tppt) REVERT: D 65 ASP cc_start: 0.9132 (t0) cc_final: 0.8879 (t0) REVERT: E 73 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8462 (mt-10) REVERT: G 39 TYR cc_start: 0.8421 (m-80) cc_final: 0.8085 (m-80) REVERT: G 92 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8165 (mm-30) REVERT: G 94 ASN cc_start: 0.9385 (t0) cc_final: 0.9100 (m-40) REVERT: H 65 ASP cc_start: 0.9225 (t0) cc_final: 0.9002 (t0) REVERT: H 68 GLU cc_start: 0.9138 (tp30) cc_final: 0.8730 (tp30) REVERT: H 80 TYR cc_start: 0.7961 (m-10) cc_final: 0.7729 (m-80) REVERT: H 102 GLU cc_start: 0.7978 (tp30) cc_final: 0.7377 (tp30) outliers start: 19 outliers final: 16 residues processed: 180 average time/residue: 0.3661 time to fit residues: 91.4520 Evaluate side-chains 175 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain M residue 50 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 104 optimal weight: 50.0000 chunk 91 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 45 optimal weight: 0.1980 chunk 92 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS H 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.052834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.037793 restraints weight = 73331.838| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.88 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13366 Z= 0.181 Angle : 0.609 10.161 19335 Z= 0.351 Chirality : 0.035 0.189 2229 Planarity : 0.004 0.050 1440 Dihedral : 30.250 118.723 4132 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.04 % Allowed : 24.47 % Favored : 72.49 % 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: 2.28 (0.29), residues: 840 helix: 2.31 (0.22), residues: 564 sheet: 2.64 (1.26), residues: 21 loop : -0.44 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 25 HIS 0.002 0.001 HIS G 31 PHE 0.007 0.001 PHE E 78 TYR 0.028 0.002 TYR H 37 ARG 0.006 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 803) hydrogen bonds : angle 3.21316 ( 2016) metal coordination : bond 0.00893 ( 4) metal coordination : angle 2.38548 ( 6) covalent geometry : bond 0.00400 (13362) covalent geometry : angle 0.60747 (19329) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 THR cc_start: 0.9541 (m) cc_final: 0.9310 (p) REVERT: B 59 LYS cc_start: 0.9292 (tmtt) cc_final: 0.8980 (tmtt) REVERT: C 64 GLU cc_start: 0.8762 (tp30) cc_final: 0.8516 (tm-30) REVERT: C 90 ASP cc_start: 0.8102 (t0) cc_final: 0.7720 (t0) REVERT: D 43 LYS cc_start: 0.9328 (mmtm) cc_final: 0.8980 (tppt) REVERT: D 65 ASP cc_start: 0.9127 (t0) cc_final: 0.8896 (t0) REVERT: D 85 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8945 (p) REVERT: E 76 GLN cc_start: 0.9053 (mp10) cc_final: 0.8838 (mp10) REVERT: F 92 ARG cc_start: 0.9419 (OUTLIER) cc_final: 0.9036 (ttp80) REVERT: G 39 TYR cc_start: 0.8416 (m-80) cc_final: 0.7522 (m-80) REVERT: G 92 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8170 (mm-30) REVERT: G 94 ASN cc_start: 0.9399 (t0) cc_final: 0.9024 (m-40) REVERT: G 110 ASN cc_start: 0.9377 (p0) cc_final: 0.9170 (p0) REVERT: H 65 ASP cc_start: 0.9169 (t0) cc_final: 0.8963 (t0) REVERT: H 68 GLU cc_start: 0.9132 (tp30) cc_final: 0.8388 (tp30) REVERT: H 80 TYR cc_start: 0.7926 (m-10) cc_final: 0.7710 (m-80) REVERT: H 90 GLU cc_start: 0.8910 (mp0) cc_final: 0.8678 (mp0) REVERT: H 102 GLU cc_start: 0.7874 (tp30) cc_final: 0.7168 (tp30) outliers start: 20 outliers final: 14 residues processed: 177 average time/residue: 0.2879 time to fit residues: 70.0660 Evaluate side-chains 175 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain M residue 50 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 5 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.053245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.038164 restraints weight = 73336.448| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.02 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13366 Z= 0.161 Angle : 0.604 8.998 19335 Z= 0.348 Chirality : 0.034 0.184 2229 Planarity : 0.004 0.051 1440 Dihedral : 30.175 118.092 4132 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.19 % Allowed : 25.38 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.29), residues: 840 helix: 2.29 (0.22), residues: 564 sheet: 2.82 (1.24), residues: 21 loop : -0.47 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 25 HIS 0.003 0.001 HIS B 75 PHE 0.006 0.001 PHE B 61 TYR 0.028 0.002 TYR H 37 ARG 0.004 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 803) hydrogen bonds : angle 3.14606 ( 2016) metal coordination : bond 0.00715 ( 4) metal coordination : angle 2.26445 ( 6) covalent geometry : bond 0.00353 (13362) covalent geometry : angle 0.60324 (19329) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8641 (mtm) cc_final: 0.7989 (mtm) REVERT: B 54 THR cc_start: 0.9574 (m) cc_final: 0.9333 (p) REVERT: B 59 LYS cc_start: 0.9283 (tmtt) cc_final: 0.8910 (tmtt) REVERT: C 64 GLU cc_start: 0.8830 (tp30) cc_final: 0.8604 (tm-30) REVERT: D 43 LYS cc_start: 0.9327 (mmtm) cc_final: 0.8952 (tppt) REVERT: D 65 ASP cc_start: 0.9239 (t0) cc_final: 0.8992 (t0) REVERT: F 79 LYS cc_start: 0.9334 (mtmm) cc_final: 0.8681 (mtmm) REVERT: F 92 ARG cc_start: 0.9441 (OUTLIER) cc_final: 0.9079 (ttp80) REVERT: G 39 TYR cc_start: 0.8442 (m-80) cc_final: 0.8192 (m-80) REVERT: G 92 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8092 (mm-30) REVERT: G 94 ASN cc_start: 0.9380 (t0) cc_final: 0.9035 (m-40) REVERT: G 110 ASN cc_start: 0.9374 (p0) cc_final: 0.9150 (p0) REVERT: H 65 ASP cc_start: 0.9287 (t0) cc_final: 0.9042 (t0) REVERT: H 68 GLU cc_start: 0.9189 (tp30) cc_final: 0.8894 (tp30) REVERT: H 80 TYR cc_start: 0.7849 (m-10) cc_final: 0.7560 (m-80) REVERT: H 90 GLU cc_start: 0.9010 (mp0) cc_final: 0.8693 (mp0) REVERT: H 102 GLU cc_start: 0.7925 (tp30) cc_final: 0.7212 (tp30) outliers start: 21 outliers final: 13 residues processed: 183 average time/residue: 0.2898 time to fit residues: 72.5128 Evaluate side-chains 175 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain M residue 50 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS H 106 HIS 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 = 0.053179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.038253 restraints weight = 73329.907| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.02 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13366 Z= 0.164 Angle : 0.613 10.493 19335 Z= 0.352 Chirality : 0.034 0.188 2229 Planarity : 0.004 0.051 1440 Dihedral : 30.106 117.749 4132 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.13 % Allowed : 26.60 % Favored : 71.28 % 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: 840 helix: 2.26 (0.22), residues: 564 sheet: 1.63 (1.20), residues: 25 loop : -0.44 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 25 HIS 0.003 0.001 HIS B 75 PHE 0.006 0.001 PHE E 78 TYR 0.027 0.002 TYR H 37 ARG 0.005 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 803) hydrogen bonds : angle 3.13540 ( 2016) metal coordination : bond 0.00697 ( 4) metal coordination : angle 2.28671 ( 6) covalent geometry : bond 0.00361 (13362) covalent geometry : angle 0.61198 (19329) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8753 (mm-30) REVERT: A 120 MET cc_start: 0.8661 (mtm) cc_final: 0.7901 (mtm) REVERT: B 54 THR cc_start: 0.9574 (m) cc_final: 0.9316 (p) REVERT: B 59 LYS cc_start: 0.9238 (tmtt) cc_final: 0.8863 (tmtt) REVERT: C 64 GLU cc_start: 0.8846 (tp30) cc_final: 0.8644 (tm-30) REVERT: D 43 LYS cc_start: 0.9311 (mmtm) cc_final: 0.8960 (tppt) REVERT: D 65 ASP cc_start: 0.9243 (t0) cc_final: 0.8999 (t0) REVERT: D 68 GLU cc_start: 0.9106 (tp30) cc_final: 0.8707 (tp30) REVERT: E 76 GLN cc_start: 0.9083 (mt0) cc_final: 0.8821 (mp10) REVERT: F 79 LYS cc_start: 0.9332 (mtmm) cc_final: 0.8681 (mtmm) REVERT: F 92 ARG cc_start: 0.9415 (OUTLIER) cc_final: 0.9054 (ttp80) REVERT: G 39 TYR cc_start: 0.8433 (m-80) cc_final: 0.8036 (m-80) REVERT: G 92 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8247 (mm-30) REVERT: G 94 ASN cc_start: 0.9376 (t0) cc_final: 0.9053 (t0) REVERT: G 110 ASN cc_start: 0.9366 (p0) cc_final: 0.9154 (p0) REVERT: H 65 ASP cc_start: 0.9300 (t0) cc_final: 0.9054 (t0) REVERT: H 68 GLU cc_start: 0.9180 (tp30) cc_final: 0.8737 (tp30) REVERT: H 73 GLU cc_start: 0.9332 (tp30) cc_final: 0.8810 (tp30) REVERT: H 80 TYR cc_start: 0.7774 (m-10) cc_final: 0.7491 (m-80) REVERT: H 90 GLU cc_start: 0.9018 (mp0) cc_final: 0.8684 (mp0) REVERT: H 102 GLU cc_start: 0.7930 (tp30) cc_final: 0.7190 (tp30) outliers start: 14 outliers final: 9 residues processed: 175 average time/residue: 0.2946 time to fit residues: 70.6874 Evaluate side-chains 173 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 0.0030 chunk 60 optimal weight: 4.9990 chunk 16 optimal weight: 0.0270 chunk 90 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.8054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.051711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.036562 restraints weight = 74195.842| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.93 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13366 Z= 0.247 Angle : 0.650 11.190 19335 Z= 0.371 Chirality : 0.036 0.198 2229 Planarity : 0.004 0.049 1440 Dihedral : 30.216 117.118 4132 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.28 % Allowed : 26.60 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.29), residues: 840 helix: 2.18 (0.22), residues: 564 sheet: 2.93 (1.22), residues: 21 loop : -0.58 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP M 25 HIS 0.005 0.001 HIS B 75 PHE 0.006 0.001 PHE B 61 TYR 0.042 0.002 TYR H 37 ARG 0.009 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.05067 ( 803) hydrogen bonds : angle 3.36386 ( 2016) metal coordination : bond 0.01202 ( 4) metal coordination : angle 2.84804 ( 6) covalent geometry : bond 0.00557 (13362) covalent geometry : angle 0.64834 (19329) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8712 (mtm) cc_final: 0.8066 (mtm) REVERT: B 54 THR cc_start: 0.9584 (m) cc_final: 0.9328 (p) REVERT: B 59 LYS cc_start: 0.9279 (tmtt) cc_final: 0.8932 (tmtt) REVERT: C 64 GLU cc_start: 0.8848 (tp30) cc_final: 0.8645 (tm-30) REVERT: D 43 LYS cc_start: 0.9309 (mmtm) cc_final: 0.8944 (tppt) REVERT: D 85 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8768 (p) REVERT: G 92 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8387 (mm-30) REVERT: H 65 ASP cc_start: 0.9232 (t0) cc_final: 0.8987 (t0) REVERT: H 68 GLU cc_start: 0.9150 (tp30) cc_final: 0.8691 (tp30) REVERT: H 73 GLU cc_start: 0.9244 (tp30) cc_final: 0.8966 (tp30) REVERT: H 76 ARG cc_start: 0.9030 (mtm-85) cc_final: 0.8569 (ptp90) REVERT: H 90 GLU cc_start: 0.8969 (mp0) cc_final: 0.8705 (mp0) REVERT: H 102 GLU cc_start: 0.8005 (tp30) cc_final: 0.7353 (tp30) outliers start: 15 outliers final: 11 residues processed: 164 average time/residue: 0.2932 time to fit residues: 65.9712 Evaluate side-chains 161 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 77 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 0.0470 chunk 29 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.051892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.036366 restraints weight = 75495.550| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.10 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13366 Z= 0.205 Angle : 0.641 10.618 19335 Z= 0.364 Chirality : 0.036 0.197 2229 Planarity : 0.004 0.049 1440 Dihedral : 30.273 115.198 4132 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.98 % Allowed : 26.75 % Favored : 71.28 % 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: 2.03 (0.29), residues: 840 helix: 2.13 (0.22), residues: 564 sheet: 3.06 (1.22), residues: 21 loop : -0.63 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP M 25 HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE B 61 TYR 0.024 0.002 TYR G 57 ARG 0.007 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04449 ( 803) hydrogen bonds : angle 3.28603 ( 2016) metal coordination : bond 0.00998 ( 4) metal coordination : angle 2.49485 ( 6) covalent geometry : bond 0.00459 (13362) covalent geometry : angle 0.63986 (19329) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4509.29 seconds wall clock time: 80 minutes 2.83 seconds (4802.83 seconds total)