Starting phenix.real_space_refine on Wed May 14 22:11:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dg3_46822/05_2025/9dg3_46822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dg3_46822/05_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_46822/05_2025/9dg3_46822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dg3_46822/05_2025/9dg3_46822.map" model { file = "/net/cci-nas-00/data/ceres_data/9dg3_46822/05_2025/9dg3_46822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dg3_46822/05_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-5687/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: 7.40, per 1000 atoms: 0.59 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: 2.94 Conformation dependent library (CDL) restraints added in 919.0 milliseconds 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: 6.02 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: 4.43 Time building geometry restraints manager: 3.47 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: 1.100 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: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.980 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: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.330 ------------------------------------------------------------------------------- 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 : 0.885 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: 0.2731 time to fit residues: 67.0784 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 : 0.896 ------------------------------------------------------------------------------- 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 = 53)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.039761 restraints weight = 73313.155| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.99 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 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 : 0.980 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8592 (tp30) cc_final: 0.8292 (tm-30) REVERT: C 92 GLU cc_start: 0.8128 (pm20) cc_final: 0.7728 (pm20) REVERT: D 65 ASP cc_start: 0.9055 (t0) cc_final: 0.8795 (t0) REVERT: F 53 GLU cc_start: 0.9361 (tp30) cc_final: 0.9013 (tp30) REVERT: H 31 LYS cc_start: 0.8841 (ttpp) cc_final: 0.8457 (pttm) REVERT: H 65 ASP cc_start: 0.9164 (t0) cc_final: 0.8919 (t0) REVERT: H 68 GLU cc_start: 0.9032 (tp30) cc_final: 0.8723 (tp30) REVERT: H 80 TYR cc_start: 0.8035 (m-10) cc_final: 0.7684 (m-80) outliers start: 14 outliers final: 9 residues processed: 174 average time/residue: 0.2617 time to fit residues: 63.7154 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 : 0.997 ------------------------------------------------------------------------------- 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: 1.9990 chunk 40 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.0980 chunk 86 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3461 r_free = 0.3461 target = 0.053762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.039116 restraints weight = 73417.346| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.82 r_work: 0.2746 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13366 Z= 0.202 Angle : 0.597 6.497 19335 Z= 0.354 Chirality : 0.036 0.178 2229 Planarity : 0.005 0.054 1440 Dihedral : 30.348 124.602 4132 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.98 % Allowed : 19.91 % Favored : 78.12 % 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: 1.97 (0.29), residues: 840 helix: 2.07 (0.22), residues: 560 sheet: 1.23 (1.13), residues: 25 loop : -0.41 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP M 25 HIS 0.005 0.001 HIS B 75 PHE 0.006 0.001 PHE E 78 TYR 0.019 0.002 TYR G 57 ARG 0.004 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 803) hydrogen bonds : angle 3.36780 ( 2016) metal coordination : bond 0.01023 ( 4) metal coordination : angle 2.64626 ( 6) covalent geometry : bond 0.00446 (13362) covalent geometry : angle 0.59574 (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 182 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.9004 (tt0) cc_final: 0.8160 (tm-30) REVERT: C 64 GLU cc_start: 0.9091 (tp30) cc_final: 0.8674 (tm-30) REVERT: C 90 ASP cc_start: 0.8497 (t0) cc_final: 0.8204 (t0) REVERT: D 43 LYS cc_start: 0.9482 (mmtm) cc_final: 0.9104 (tppt) REVERT: D 65 ASP cc_start: 0.9282 (t0) cc_final: 0.9042 (t0) REVERT: D 90 GLU cc_start: 0.8676 (mp0) cc_final: 0.8457 (mp0) REVERT: E 74 ILE cc_start: 0.9537 (OUTLIER) cc_final: 0.9333 (mp) REVERT: E 76 GLN cc_start: 0.9084 (mp10) cc_final: 0.8822 (mp10) REVERT: F 53 GLU cc_start: 0.9481 (tp30) cc_final: 0.9150 (tp30) REVERT: G 110 ASN cc_start: 0.9478 (p0) cc_final: 0.9272 (p0) REVERT: H 65 ASP cc_start: 0.9424 (t0) cc_final: 0.9178 (t0) REVERT: H 68 GLU cc_start: 0.9406 (tp30) cc_final: 0.9192 (tp30) REVERT: H 80 TYR cc_start: 0.8277 (m-10) cc_final: 0.7937 (m-80) outliers start: 13 outliers final: 7 residues processed: 176 average time/residue: 0.2753 time to fit residues: 67.3462 Evaluate side-chains 163 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 74 ILE 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: 0.8980 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 103 optimal weight: 30.0000 chunk 55 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3473 r_free = 0.3473 target = 0.054079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.039044 restraints weight = 72020.998| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.01 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13366 Z= 0.154 Angle : 0.588 10.819 19335 Z= 0.345 Chirality : 0.035 0.161 2229 Planarity : 0.004 0.054 1440 Dihedral : 30.222 122.523 4132 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.13 % Allowed : 20.97 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.29), residues: 840 helix: 2.17 (0.22), residues: 564 sheet: 1.36 (1.15), residues: 25 loop : -0.34 (0.36), residues: 251 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 0.008 0.001 PHE D 67 TYR 0.035 0.002 TYR F 88 ARG 0.010 0.001 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 803) hydrogen bonds : angle 3.17525 ( 2016) metal coordination : bond 0.00671 ( 4) metal coordination : angle 2.10829 ( 6) covalent geometry : bond 0.00332 (13362) covalent geometry : angle 0.58708 (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 191 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8462 (mtm) cc_final: 0.7974 (mtm) REVERT: B 54 THR cc_start: 0.9580 (m) cc_final: 0.9215 (p) REVERT: B 67 ARG cc_start: 0.9028 (ttp80) cc_final: 0.8471 (ttm-80) REVERT: C 64 GLU cc_start: 0.8785 (tp30) cc_final: 0.8401 (tm-30) REVERT: C 90 ASP cc_start: 0.8090 (t0) cc_final: 0.7620 (t0) REVERT: D 43 LYS cc_start: 0.9356 (mmtm) cc_final: 0.8943 (tppt) REVERT: D 65 ASP cc_start: 0.9163 (t0) cc_final: 0.8942 (t0) REVERT: D 68 GLU cc_start: 0.9129 (tp30) cc_final: 0.8710 (tp30) REVERT: D 90 GLU cc_start: 0.8447 (mp0) cc_final: 0.8207 (mp0) REVERT: E 76 GLN cc_start: 0.8829 (mp10) cc_final: 0.8515 (mp10) REVERT: E 125 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.8912 (mp10) REVERT: G 39 TYR cc_start: 0.8370 (m-80) cc_final: 0.8053 (m-80) REVERT: G 92 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8184 (mt-10) REVERT: G 94 ASN cc_start: 0.9378 (OUTLIER) cc_final: 0.9002 (m-40) REVERT: G 95 LYS cc_start: 0.9517 (tptm) cc_final: 0.9306 (tttm) REVERT: G 110 ASN cc_start: 0.9420 (p0) cc_final: 0.9219 (p0) REVERT: H 65 ASP cc_start: 0.9333 (t0) cc_final: 0.9056 (t0) REVERT: H 68 GLU cc_start: 0.9200 (tp30) cc_final: 0.8917 (tp30) REVERT: H 80 TYR cc_start: 0.8048 (m-10) cc_final: 0.7796 (m-80) outliers start: 14 outliers final: 4 residues processed: 187 average time/residue: 0.2615 time to fit residues: 67.7105 Evaluate side-chains 170 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.8980 chunk 64 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 104 optimal weight: 50.0000 chunk 103 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.052031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.036441 restraints weight = 73800.472| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.96 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 13366 Z= 0.248 Angle : 0.622 7.996 19335 Z= 0.364 Chirality : 0.036 0.172 2229 Planarity : 0.005 0.051 1440 Dihedral : 30.326 120.756 4132 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.43 % Allowed : 22.49 % 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: 2.14 (0.29), residues: 840 helix: 2.18 (0.22), residues: 565 sheet: 2.27 (1.24), residues: 21 loop : -0.41 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP M 25 HIS 0.006 0.002 HIS F 75 PHE 0.011 0.001 PHE B 61 TYR 0.020 0.002 TYR G 57 ARG 0.004 0.001 ARG F 67 Details of bonding type rmsd hydrogen bonds : bond 0.05377 ( 803) hydrogen bonds : angle 3.40824 ( 2016) metal coordination : bond 0.01392 ( 4) metal coordination : angle 2.95473 ( 6) covalent geometry : bond 0.00554 (13362) covalent geometry : angle 0.62034 (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 172 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8656 (mtm) cc_final: 0.8308 (mtm) REVERT: A 125 GLN cc_start: 0.9297 (mt0) cc_final: 0.9077 (mt0) REVERT: C 64 GLU cc_start: 0.8784 (tp30) cc_final: 0.8464 (tm-30) REVERT: C 90 ASP cc_start: 0.8178 (t0) cc_final: 0.7814 (t0) REVERT: D 43 LYS cc_start: 0.9378 (mmtm) cc_final: 0.9015 (tppt) REVERT: D 85 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8791 (p) REVERT: D 90 GLU cc_start: 0.8399 (mp0) cc_final: 0.8119 (mp0) REVERT: E 76 GLN cc_start: 0.8771 (mp10) cc_final: 0.8451 (mp10) REVERT: G 92 GLU cc_start: 0.8657 (tt0) cc_final: 0.8370 (mm-30) REVERT: H 65 ASP cc_start: 0.9283 (t0) cc_final: 0.8996 (t0) REVERT: H 68 GLU cc_start: 0.9139 (tp30) cc_final: 0.8885 (tp30) REVERT: H 80 TYR cc_start: 0.8183 (m-10) cc_final: 0.7776 (m-80) outliers start: 16 outliers final: 11 residues processed: 166 average time/residue: 0.2698 time to fit residues: 61.4780 Evaluate side-chains 158 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 113 LYS 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: 3.9990 chunk 83 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.0370 chunk 82 optimal weight: 5.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- 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 H 46 HIS H 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.053248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.038130 restraints weight = 73620.910| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.02 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13366 Z= 0.161 Angle : 0.591 8.330 19335 Z= 0.345 Chirality : 0.034 0.169 2229 Planarity : 0.004 0.051 1440 Dihedral : 30.311 118.353 4132 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.28 % Allowed : 23.56 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.29), residues: 840 helix: 2.31 (0.22), residues: 564 sheet: 1.70 (1.19), residues: 24 loop : -0.41 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 25 HIS 0.005 0.001 HIS B 75 PHE 0.007 0.001 PHE D 67 TYR 0.033 0.002 TYR B 88 ARG 0.003 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 803) hydrogen bonds : angle 3.15023 ( 2016) metal coordination : bond 0.00762 ( 4) metal coordination : angle 2.26600 ( 6) covalent geometry : bond 0.00351 (13362) covalent geometry : angle 0.58966 (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 183 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8738 (mtm) cc_final: 0.8132 (mtm) REVERT: A 125 GLN cc_start: 0.9361 (mt0) cc_final: 0.9119 (mt0) REVERT: C 64 GLU cc_start: 0.8793 (tp30) cc_final: 0.8558 (tm-30) REVERT: C 90 ASP cc_start: 0.8006 (t0) cc_final: 0.7598 (t0) REVERT: D 43 LYS cc_start: 0.9378 (mmtm) cc_final: 0.9010 (tppt) REVERT: D 65 ASP cc_start: 0.9224 (t0) cc_final: 0.8986 (t0) REVERT: D 85 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8699 (p) REVERT: D 90 GLU cc_start: 0.8475 (mp0) cc_final: 0.8095 (mp0) REVERT: E 73 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8680 (mt-10) REVERT: F 92 ARG cc_start: 0.9397 (mtp-110) cc_final: 0.9062 (ttp80) REVERT: G 39 TYR cc_start: 0.8364 (m-80) cc_final: 0.7896 (m-80) REVERT: G 92 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8335 (mt-10) REVERT: G 94 ASN cc_start: 0.9179 (OUTLIER) cc_final: 0.8892 (m-40) REVERT: G 110 ASN cc_start: 0.9371 (p0) cc_final: 0.9140 (p0) REVERT: H 65 ASP cc_start: 0.9266 (t0) cc_final: 0.9023 (t0) REVERT: H 68 GLU cc_start: 0.9204 (tp30) cc_final: 0.8777 (tp30) REVERT: H 80 TYR cc_start: 0.7951 (m-10) cc_final: 0.7743 (m-80) outliers start: 15 outliers final: 8 residues processed: 180 average time/residue: 0.2911 time to fit residues: 71.0552 Evaluate side-chains 170 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 104 optimal weight: 50.0000 chunk 91 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 107 optimal weight: 30.0000 chunk 45 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 E 76 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** H 106 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 = 0.3421 r_free = 0.3421 target = 0.052011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.036810 restraints weight = 73715.431| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.91 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13366 Z= 0.240 Angle : 0.629 9.868 19335 Z= 0.361 Chirality : 0.036 0.177 2229 Planarity : 0.004 0.049 1440 Dihedral : 30.269 118.362 4132 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.04 % Allowed : 24.01 % Favored : 72.95 % 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: 2.30 (0.22), residues: 563 sheet: 2.54 (1.23), residues: 21 loop : -0.52 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP M 25 HIS 0.009 0.001 HIS B 75 PHE 0.009 0.001 PHE B 61 TYR 0.031 0.002 TYR B 88 ARG 0.006 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.04990 ( 803) hydrogen bonds : angle 3.35374 ( 2016) metal coordination : bond 0.01244 ( 4) metal coordination : angle 2.95072 ( 6) covalent geometry : bond 0.00536 (13362) covalent geometry : angle 0.62685 (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 176 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8748 (mtm) cc_final: 0.8091 (mtm) REVERT: C 64 GLU cc_start: 0.8815 (tp30) cc_final: 0.8566 (tm-30) REVERT: D 43 LYS cc_start: 0.9344 (mmtm) cc_final: 0.8980 (tppt) REVERT: D 65 ASP cc_start: 0.9165 (t0) cc_final: 0.8904 (t0) REVERT: E 76 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8622 (mp10) REVERT: G 39 TYR cc_start: 0.8503 (m-80) cc_final: 0.7680 (m-80) REVERT: G 92 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.6398 (pt0) REVERT: G 94 ASN cc_start: 0.9291 (OUTLIER) cc_final: 0.8885 (m-40) REVERT: H 65 ASP cc_start: 0.9185 (t0) cc_final: 0.8964 (t0) REVERT: H 68 GLU cc_start: 0.9133 (tp30) cc_final: 0.8424 (tp30) REVERT: H 80 TYR cc_start: 0.8006 (m-10) cc_final: 0.7752 (m-80) REVERT: H 90 GLU cc_start: 0.8903 (mp0) cc_final: 0.8616 (mp0) outliers start: 20 outliers final: 13 residues processed: 168 average time/residue: 0.2793 time to fit residues: 64.4283 Evaluate side-chains 163 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 115 LYS 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 G residue 94 ASN Chi-restraints excluded: chain H residue 113 LYS 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: 8.9990 chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 75 HIS E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 46 HIS H 106 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.052462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.037479 restraints weight = 75460.694| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.09 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13366 Z= 0.169 Angle : 0.623 10.456 19335 Z= 0.356 Chirality : 0.035 0.189 2229 Planarity : 0.004 0.050 1440 Dihedral : 30.254 116.893 4132 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.13 % Allowed : 25.99 % Favored : 71.88 % 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: 2.18 (0.29), residues: 840 helix: 2.24 (0.22), residues: 564 sheet: 2.74 (1.26), residues: 21 loop : -0.51 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 25 HIS 0.007 0.001 HIS B 75 PHE 0.006 0.001 PHE A 67 TYR 0.032 0.002 TYR B 88 ARG 0.004 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 803) hydrogen bonds : angle 3.19072 ( 2016) metal coordination : bond 0.00773 ( 4) metal coordination : angle 2.25499 ( 6) covalent geometry : bond 0.00373 (13362) covalent geometry : angle 0.62155 (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 180 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8845 (mtm) cc_final: 0.7871 (mtm) REVERT: B 54 THR cc_start: 0.9599 (m) cc_final: 0.9315 (p) REVERT: B 63 GLU cc_start: 0.8766 (tt0) cc_final: 0.8350 (tm-30) REVERT: C 64 GLU cc_start: 0.8843 (tp30) cc_final: 0.8637 (tm-30) REVERT: C 90 ASP cc_start: 0.8058 (t0) cc_final: 0.7849 (t0) REVERT: D 43 LYS cc_start: 0.9331 (mmtm) cc_final: 0.8947 (tppt) REVERT: D 65 ASP cc_start: 0.9243 (t0) cc_final: 0.8978 (t0) REVERT: D 83 ARG cc_start: 0.8753 (tpp80) cc_final: 0.8248 (tpp80) REVERT: D 90 GLU cc_start: 0.8470 (mp0) cc_final: 0.8080 (mp0) REVERT: E 76 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8762 (mp10) REVERT: F 92 ARG cc_start: 0.9444 (OUTLIER) cc_final: 0.9088 (ttp80) REVERT: G 38 ASN cc_start: 0.8959 (p0) cc_final: 0.8681 (p0) REVERT: G 39 TYR cc_start: 0.8512 (m-80) cc_final: 0.8113 (m-80) REVERT: G 94 ASN cc_start: 0.9295 (OUTLIER) cc_final: 0.8735 (m-40) REVERT: H 65 ASP cc_start: 0.9293 (t0) cc_final: 0.9042 (t0) REVERT: H 68 GLU cc_start: 0.9203 (tp30) cc_final: 0.8752 (tp30) REVERT: H 80 TYR cc_start: 0.7897 (m-10) cc_final: 0.7684 (m-80) REVERT: H 90 GLU cc_start: 0.9003 (mp0) cc_final: 0.8716 (mp0) outliers start: 14 outliers final: 11 residues processed: 176 average time/residue: 0.2828 time to fit residues: 67.9509 Evaluate side-chains 170 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 76 GLN Chi-restraints excluded: chain E residue 80 THR 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 94 ASN Chi-restraints excluded: chain H residue 106 HIS 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: 10.0000 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 106 optimal weight: 0.0030 chunk 8 optimal weight: 1.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN E 76 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 46 HIS H 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.051954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.036706 restraints weight = 75729.650| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.04 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3120 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= 0.200 Angle : 0.633 11.117 19335 Z= 0.362 Chirality : 0.035 0.186 2229 Planarity : 0.004 0.050 1440 Dihedral : 30.213 116.902 4132 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.43 % Allowed : 25.68 % Favored : 71.88 % 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: 2.18 (0.29), residues: 840 helix: 2.24 (0.22), residues: 564 sheet: 2.73 (1.24), residues: 21 loop : -0.53 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP M 25 HIS 0.004 0.001 HIS H 106 PHE 0.006 0.001 PHE D 67 TYR 0.034 0.002 TYR B 88 ARG 0.004 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 803) hydrogen bonds : angle 3.25959 ( 2016) metal coordination : bond 0.00996 ( 4) metal coordination : angle 2.54867 ( 6) covalent geometry : bond 0.00446 (13362) covalent geometry : angle 0.63176 (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 169 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8862 (mtm) cc_final: 0.7923 (mtm) REVERT: C 64 GLU cc_start: 0.8834 (tp30) cc_final: 0.8630 (tm-30) REVERT: D 43 LYS cc_start: 0.9328 (mmtm) cc_final: 0.8964 (tppt) REVERT: D 65 ASP cc_start: 0.9200 (t0) cc_final: 0.8937 (t0) REVERT: E 76 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8731 (mp10) REVERT: F 92 ARG cc_start: 0.9464 (OUTLIER) cc_final: 0.9076 (ttp80) REVERT: G 39 TYR cc_start: 0.8555 (m-80) cc_final: 0.7746 (m-80) REVERT: G 92 GLU cc_start: 0.8831 (tp30) cc_final: 0.8541 (mm-30) REVERT: G 94 ASN cc_start: 0.9334 (OUTLIER) cc_final: 0.8749 (m-40) REVERT: H 65 ASP cc_start: 0.9222 (t0) cc_final: 0.8941 (t0) REVERT: H 68 GLU cc_start: 0.9157 (tp30) cc_final: 0.8479 (tp30) REVERT: H 80 TYR cc_start: 0.7945 (m-10) cc_final: 0.7640 (m-80) outliers start: 16 outliers final: 9 residues processed: 164 average time/residue: 0.2652 time to fit residues: 59.9389 Evaluate side-chains 164 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 76 GLN Chi-restraints excluded: chain E residue 80 THR 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 94 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 0.1980 chunk 60 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** 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 = 0.3410 r_free = 0.3410 target = 0.051633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.036633 restraints weight = 73593.553| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.88 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13366 Z= 0.243 Angle : 0.672 11.983 19335 Z= 0.378 Chirality : 0.037 0.193 2229 Planarity : 0.004 0.049 1440 Dihedral : 30.276 116.455 4132 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.28 % Allowed : 26.44 % 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: 2.11 (0.29), residues: 840 helix: 2.21 (0.22), residues: 564 sheet: 2.73 (1.25), residues: 21 loop : -0.62 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP M 25 HIS 0.004 0.001 HIS B 75 PHE 0.006 0.001 PHE B 61 TYR 0.036 0.002 TYR B 88 ARG 0.005 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 803) hydrogen bonds : angle 3.37144 ( 2016) metal coordination : bond 0.01234 ( 4) metal coordination : angle 2.80403 ( 6) covalent geometry : bond 0.00544 (13362) covalent geometry : angle 0.67006 (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 169 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8885 (mtm) cc_final: 0.7938 (mtm) REVERT: C 64 GLU cc_start: 0.8865 (tp30) cc_final: 0.8642 (tm-30) REVERT: D 43 LYS cc_start: 0.9328 (mmtm) cc_final: 0.8953 (tppt) REVERT: D 65 ASP cc_start: 0.9217 (t0) cc_final: 0.8931 (t0) REVERT: E 107 THR cc_start: 0.9384 (m) cc_final: 0.9139 (p) REVERT: G 94 ASN cc_start: 0.9352 (OUTLIER) cc_final: 0.8720 (m-40) REVERT: H 65 ASP cc_start: 0.9239 (t0) cc_final: 0.8998 (t0) REVERT: H 68 GLU cc_start: 0.9144 (tp30) cc_final: 0.8835 (tp30) REVERT: H 80 TYR cc_start: 0.7914 (m-10) cc_final: 0.7676 (m-80) REVERT: H 90 GLU cc_start: 0.8974 (mp0) cc_final: 0.8691 (mp0) outliers start: 15 outliers final: 12 residues processed: 164 average time/residue: 0.2747 time to fit residues: 62.0954 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 : 0.914 ------------------------------------------------------------------------------- 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 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 80 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 94 ASN 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: 1.9990 chunk 107 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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** G 94 ASN H 46 HIS ** H 106 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 = 0.3384 r_free = 0.3384 target = 0.051030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.036069 restraints weight = 76070.825| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.05 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13366 Z= 0.233 Angle : 0.664 11.191 19335 Z= 0.378 Chirality : 0.037 0.196 2229 Planarity : 0.004 0.049 1440 Dihedral : 30.404 114.642 4132 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.28 % Allowed : 26.90 % Favored : 70.82 % 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: 2.02 (0.29), residues: 840 helix: 2.18 (0.22), residues: 564 sheet: 0.95 (1.54), residues: 12 loop : -0.52 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP M 25 HIS 0.004 0.001 HIS B 75 PHE 0.014 0.001 PHE E 78 TYR 0.036 0.002 TYR B 88 ARG 0.004 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.04864 ( 803) hydrogen bonds : angle 3.45761 ( 2016) metal coordination : bond 0.01189 ( 4) metal coordination : angle 2.67474 ( 6) covalent geometry : bond 0.00522 (13362) covalent geometry : angle 0.66264 (19329) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4582.24 seconds wall clock time: 80 minutes 13.14 seconds (4813.14 seconds total)