Starting phenix.real_space_refine on Sat Jan 18 13:27:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dg3_46822/01_2025/9dg3_46822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dg3_46822/01_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_46822/01_2025/9dg3_46822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dg3_46822/01_2025/9dg3_46822.map" model { file = "/net/cci-nas-00/data/ceres_data/9dg3_46822/01_2025/9dg3_46822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dg3_46822/01_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-5571/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: 7.59, per 1000 atoms: 0.60 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: 3.31 Conformation dependent library (CDL) restraints added in 1.0 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: 5.84 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: 4.58 Time building geometry restraints manager: 3.80 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 36.090 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.060 ------------------------------------------------------------------------------- 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 13362 Z= 0.292 Angle : 0.789 10.752 19329 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 *********************** 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 : 0.993 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: 0.3000 time to fit residues: 73.2669 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 : 0.970 ------------------------------------------------------------------------------- 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 13362 Z= 0.239 Angle : 0.617 10.940 19329 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 *********************** 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 : 0.906 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: 0.2781 time to fit residues: 67.1354 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 : 1.048 ------------------------------------------------------------------------------- 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: 0.0570 chunk 86 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.053706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.038833 restraints weight = 74179.861| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.97 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13362 Z= 0.244 Angle : 0.590 6.449 19329 Z= 0.351 Chirality : 0.035 0.182 2229 Planarity : 0.005 0.054 1440 Dihedral : 30.314 124.541 4132 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.98 % Allowed : 20.06 % Favored : 77.96 % 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: 1.99 (0.29), residues: 840 helix: 2.09 (0.22), residues: 560 sheet: 1.27 (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 0.016 0.002 TYR G 57 ARG 0.004 0.000 ARG E 116 *********************** 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 : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8652 (tt0) cc_final: 0.7787 (tm-30) REVERT: C 64 GLU cc_start: 0.8746 (tp30) cc_final: 0.8329 (tm-30) REVERT: C 90 ASP cc_start: 0.8283 (t0) cc_final: 0.7948 (t0) REVERT: D 43 LYS cc_start: 0.9340 (mmtm) cc_final: 0.8894 (tppt) REVERT: D 65 ASP cc_start: 0.9118 (t0) cc_final: 0.8844 (t0) REVERT: D 90 GLU cc_start: 0.8345 (mp0) cc_final: 0.8116 (mp0) REVERT: E 76 GLN cc_start: 0.8867 (mp10) cc_final: 0.8616 (mp10) REVERT: F 53 GLU cc_start: 0.9433 (tp30) cc_final: 0.9075 (tp30) REVERT: G 39 TYR cc_start: 0.8424 (m-80) cc_final: 0.8183 (m-80) REVERT: H 65 ASP cc_start: 0.9232 (t0) cc_final: 0.8968 (t0) REVERT: H 68 GLU cc_start: 0.9138 (tp30) cc_final: 0.8874 (tp30) REVERT: H 80 TYR cc_start: 0.8047 (m-10) cc_final: 0.7822 (m-80) outliers start: 13 outliers final: 7 residues processed: 179 average time/residue: 0.2799 time to fit residues: 68.8562 Evaluate side-chains 165 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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: 0.8980 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 103 optimal weight: 30.0000 chunk 55 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3426 r_free = 0.3426 target = 0.052203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.036638 restraints weight = 73930.693| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.00 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13362 Z= 0.291 Angle : 0.611 7.808 19329 Z= 0.358 Chirality : 0.036 0.162 2229 Planarity : 0.005 0.052 1440 Dihedral : 30.338 122.287 4132 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.74 % Allowed : 21.58 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.29), residues: 840 helix: 2.16 (0.22), residues: 564 sheet: 1.18 (1.15), residues: 25 loop : -0.39 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 25 HIS 0.007 0.001 HIS B 75 PHE 0.009 0.001 PHE B 61 TYR 0.018 0.002 TYR G 57 ARG 0.004 0.000 ARG E 116 *********************** 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 170 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8610 (mtm) cc_final: 0.8243 (mtm) REVERT: C 64 GLU cc_start: 0.8778 (tp30) cc_final: 0.8469 (tm-30) REVERT: C 90 ASP cc_start: 0.8215 (t0) cc_final: 0.7821 (t0) REVERT: D 43 LYS cc_start: 0.9369 (mmtm) cc_final: 0.8967 (tppt) REVERT: D 85 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8787 (p) REVERT: D 90 GLU cc_start: 0.8424 (mp0) cc_final: 0.8171 (mp0) REVERT: E 76 GLN cc_start: 0.8824 (mp10) cc_final: 0.8508 (mp10) REVERT: F 53 GLU cc_start: 0.9426 (tp30) cc_final: 0.9087 (tp30) REVERT: G 92 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: G 94 ASN cc_start: 0.9427 (OUTLIER) cc_final: 0.9050 (m-40) REVERT: H 65 ASP cc_start: 0.9274 (t0) cc_final: 0.9001 (t0) REVERT: H 68 GLU cc_start: 0.9122 (tp30) cc_final: 0.8833 (tp30) REVERT: H 80 TYR cc_start: 0.8174 (m-10) cc_final: 0.7827 (m-80) REVERT: H 102 GLU cc_start: 0.7943 (tp30) cc_final: 0.6930 (tp30) REVERT: H 106 HIS cc_start: 0.7821 (OUTLIER) cc_final: 0.7095 (m170) outliers start: 18 outliers final: 9 residues processed: 165 average time/residue: 0.2836 time to fit residues: 64.7655 Evaluate side-chains 159 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 86 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 G residue 92 GLU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 106 HIS 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: 0.0040 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 104 optimal weight: 50.0000 chunk 103 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- 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 93 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.053116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.037963 restraints weight = 72594.664| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.83 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13362 Z= 0.206 Angle : 0.584 7.572 19329 Z= 0.344 Chirality : 0.035 0.176 2229 Planarity : 0.004 0.052 1440 Dihedral : 30.323 119.424 4132 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.98 % Allowed : 22.34 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.29), residues: 840 helix: 2.23 (0.22), residues: 564 sheet: 1.20 (1.15), residues: 25 loop : -0.40 (0.36), residues: 251 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 0.006 0.001 PHE D 67 TYR 0.020 0.002 TYR G 57 ARG 0.003 0.000 ARG F 67 *********************** 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: 13 poor density : 171 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8561 (mtm) cc_final: 0.8224 (mtm) REVERT: B 54 THR cc_start: 0.9567 (m) cc_final: 0.9260 (p) REVERT: C 64 GLU cc_start: 0.8752 (tp30) cc_final: 0.8456 (tm-30) REVERT: C 90 ASP cc_start: 0.8108 (t0) cc_final: 0.7846 (t0) REVERT: D 43 LYS cc_start: 0.9374 (mmtm) cc_final: 0.9016 (tppt) REVERT: D 65 ASP cc_start: 0.9123 (t0) cc_final: 0.8899 (t0) REVERT: D 90 GLU cc_start: 0.8393 (mp0) cc_final: 0.8115 (mp0) REVERT: E 76 GLN cc_start: 0.8726 (mp10) cc_final: 0.8391 (mp10) REVERT: G 38 ASN cc_start: 0.8923 (p0) cc_final: 0.8679 (p0) REVERT: G 94 ASN cc_start: 0.9330 (t0) cc_final: 0.9100 (t0) REVERT: G 95 LYS cc_start: 0.9504 (tptm) cc_final: 0.9299 (tttm) REVERT: H 65 ASP cc_start: 0.9216 (t0) cc_final: 0.9005 (t0) REVERT: H 68 GLU cc_start: 0.9159 (tp30) cc_final: 0.8945 (tp30) REVERT: H 80 TYR cc_start: 0.7998 (m-10) cc_final: 0.7758 (m-80) outliers start: 13 outliers final: 7 residues processed: 180 average time/residue: 0.3050 time to fit residues: 75.0707 Evaluate side-chains 165 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 27 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 0.0020 chunk 82 optimal weight: 6.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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** 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 = 0.3481 r_free = 0.3481 target = 0.054268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.039244 restraints weight = 73091.599| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.03 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13362 Z= 0.171 Angle : 0.588 11.357 19329 Z= 0.342 Chirality : 0.034 0.169 2229 Planarity : 0.004 0.053 1440 Dihedral : 30.099 119.194 4132 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: 2.25 (0.29), residues: 840 helix: 2.30 (0.22), residues: 564 sheet: 1.52 (1.18), residues: 25 loop : -0.40 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP M 25 HIS 0.005 0.001 HIS H 106 PHE 0.007 0.001 PHE D 67 TYR 0.023 0.002 TYR G 57 ARG 0.006 0.000 ARG F 67 *********************** 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 191 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.9055 (tp30) cc_final: 0.8824 (tp30) REVERT: B 54 THR cc_start: 0.9588 (m) cc_final: 0.9302 (p) REVERT: B 92 ARG cc_start: 0.9376 (OUTLIER) cc_final: 0.8572 (tmm-80) REVERT: C 64 GLU cc_start: 0.8797 (tp30) cc_final: 0.8582 (tm-30) REVERT: C 90 ASP cc_start: 0.8004 (t0) cc_final: 0.7675 (t0) REVERT: D 43 LYS cc_start: 0.9349 (mmtm) cc_final: 0.8968 (tppt) REVERT: D 65 ASP cc_start: 0.9263 (t0) cc_final: 0.9015 (t0) REVERT: D 90 GLU cc_start: 0.8481 (mp0) cc_final: 0.8088 (mp0) REVERT: E 105 GLU cc_start: 0.8749 (tp30) cc_final: 0.8546 (tp30) REVERT: F 53 GLU cc_start: 0.9457 (mm-30) cc_final: 0.8860 (mm-30) REVERT: F 74 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8590 (mm-30) REVERT: F 79 LYS cc_start: 0.9362 (mtmm) cc_final: 0.8767 (mtmm) REVERT: F 84 MET cc_start: 0.8928 (tpp) cc_final: 0.8521 (tmm) REVERT: F 92 ARG cc_start: 0.9415 (OUTLIER) cc_final: 0.9060 (ttp80) REVERT: G 39 TYR cc_start: 0.8234 (m-80) cc_final: 0.7808 (m-80) REVERT: G 92 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7939 (tp30) REVERT: H 65 ASP cc_start: 0.9265 (t0) cc_final: 0.9030 (t0) REVERT: H 68 GLU cc_start: 0.9182 (tp30) cc_final: 0.8766 (tp30) REVERT: H 80 TYR cc_start: 0.7959 (m-10) cc_final: 0.7622 (m-80) outliers start: 15 outliers final: 7 residues processed: 186 average time/residue: 0.2954 time to fit residues: 75.2367 Evaluate side-chains 176 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 107 optimal weight: 30.0000 chunk 45 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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** H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.052375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.037492 restraints weight = 74518.238| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.95 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13362 Z= 0.283 Angle : 0.617 8.277 19329 Z= 0.356 Chirality : 0.036 0.173 2229 Planarity : 0.004 0.050 1440 Dihedral : 30.150 119.127 4132 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.04 % Allowed : 24.32 % Favored : 72.64 % 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: 2.29 (0.29), residues: 840 helix: 2.34 (0.22), residues: 564 sheet: 2.60 (1.24), residues: 21 loop : -0.48 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP M 25 HIS 0.008 0.001 HIS B 75 PHE 0.008 0.001 PHE C 25 TYR 0.020 0.002 TYR D 37 ARG 0.004 0.000 ARG C 99 *********************** 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 180 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8510 (mtm) cc_final: 0.7986 (mtm) REVERT: C 64 GLU cc_start: 0.8823 (tp30) cc_final: 0.8616 (tm-30) REVERT: C 90 ASP cc_start: 0.8099 (t0) cc_final: 0.7836 (t0) REVERT: D 43 LYS cc_start: 0.9339 (mmtm) cc_final: 0.8963 (tppt) REVERT: D 65 ASP cc_start: 0.9208 (t0) cc_final: 0.8919 (t0) REVERT: D 85 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8685 (p) REVERT: D 90 GLU cc_start: 0.8447 (mp0) cc_final: 0.8042 (mp0) REVERT: E 76 GLN cc_start: 0.9054 (mt0) cc_final: 0.8696 (mp10) REVERT: G 39 TYR cc_start: 0.8431 (m-80) cc_final: 0.8180 (m-80) REVERT: G 94 ASN cc_start: 0.9406 (t0) cc_final: 0.8866 (m-40) REVERT: H 65 ASP cc_start: 0.9221 (t0) cc_final: 0.8990 (t0) REVERT: H 68 GLU cc_start: 0.9167 (tp30) cc_final: 0.8865 (tp30) REVERT: H 80 TYR cc_start: 0.7888 (m-10) cc_final: 0.7557 (m-80) REVERT: H 90 GLU cc_start: 0.8938 (mp0) cc_final: 0.8612 (mp0) outliers start: 20 outliers final: 13 residues processed: 171 average time/residue: 0.2924 time to fit residues: 68.2683 Evaluate side-chains 165 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE 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 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 H residue 77 LEU Chi-restraints excluded: chain M residue 43 ILE 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: 0.4980 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.053175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.038333 restraints weight = 74990.604| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.08 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13362 Z= 0.197 Angle : 0.607 10.485 19329 Z= 0.348 Chirality : 0.034 0.166 2229 Planarity : 0.004 0.051 1440 Dihedral : 30.116 117.037 4132 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.82 % Allowed : 26.14 % Favored : 72.04 % 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: 2.27 (0.29), residues: 840 helix: 2.30 (0.22), residues: 564 sheet: 2.82 (1.25), residues: 21 loop : -0.44 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 25 HIS 0.007 0.001 HIS B 75 PHE 0.007 0.001 PHE B 61 TYR 0.022 0.002 TYR F 88 ARG 0.006 0.000 ARG B 67 *********************** 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 176 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8515 (mtm) cc_final: 0.7826 (mtm) REVERT: B 53 GLU cc_start: 0.9102 (tp30) cc_final: 0.8886 (tp30) REVERT: B 92 ARG cc_start: 0.9410 (OUTLIER) cc_final: 0.8530 (tmm-80) REVERT: C 90 ASP cc_start: 0.8114 (t0) cc_final: 0.7753 (t0) REVERT: D 43 LYS cc_start: 0.9314 (mmtm) cc_final: 0.8953 (tppt) REVERT: D 65 ASP cc_start: 0.9244 (t0) cc_final: 0.9005 (t0) REVERT: D 85 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8613 (p) REVERT: D 90 GLU cc_start: 0.8507 (mp0) cc_final: 0.8040 (mp0) REVERT: F 74 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8641 (mm-30) REVERT: F 79 LYS cc_start: 0.9320 (mtmm) cc_final: 0.8668 (mtmm) REVERT: F 92 ARG cc_start: 0.9461 (OUTLIER) cc_final: 0.9110 (ttp80) REVERT: G 38 ASN cc_start: 0.8895 (p0) cc_final: 0.8622 (p0) REVERT: H 65 ASP cc_start: 0.9304 (t0) cc_final: 0.9066 (t0) REVERT: H 68 GLU cc_start: 0.9172 (tp30) cc_final: 0.8692 (tp30) REVERT: H 80 TYR cc_start: 0.7710 (m-10) cc_final: 0.7493 (m-80) REVERT: H 90 GLU cc_start: 0.8988 (mp0) cc_final: 0.8686 (mp0) REVERT: M 48 LYS cc_start: 0.7146 (ttpt) cc_final: 0.6944 (mttt) outliers start: 12 outliers final: 9 residues processed: 172 average time/residue: 0.2871 time to fit residues: 67.5050 Evaluate side-chains 173 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 33 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.052510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.037461 restraints weight = 74064.859| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.04 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13362 Z= 0.237 Angle : 0.626 9.392 19329 Z= 0.358 Chirality : 0.035 0.174 2229 Planarity : 0.004 0.049 1440 Dihedral : 30.084 117.254 4132 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.98 % Allowed : 25.38 % Favored : 72.64 % 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: 2.29 (0.29), residues: 840 helix: 2.32 (0.22), residues: 564 sheet: 2.94 (1.22), residues: 21 loop : -0.46 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 25 HIS 0.006 0.001 HIS B 75 PHE 0.005 0.001 PHE D 67 TYR 0.026 0.002 TYR G 39 ARG 0.005 0.000 ARG A 52 *********************** 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 176 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8750 (mm-30) REVERT: B 53 GLU cc_start: 0.9114 (tp30) cc_final: 0.8899 (tp30) REVERT: B 63 GLU cc_start: 0.8812 (tt0) cc_final: 0.7908 (tm-30) REVERT: C 90 ASP cc_start: 0.8145 (t0) cc_final: 0.7930 (t0) REVERT: D 43 LYS cc_start: 0.9320 (mmtm) cc_final: 0.8952 (tppt) REVERT: D 65 ASP cc_start: 0.9245 (t0) cc_final: 0.8973 (t0) REVERT: D 85 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8600 (p) REVERT: D 90 GLU cc_start: 0.8534 (mp0) cc_final: 0.8047 (mp0) REVERT: F 74 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8675 (mm-30) REVERT: F 79 LYS cc_start: 0.9341 (mtmm) cc_final: 0.8687 (mtmm) REVERT: G 38 ASN cc_start: 0.8852 (p0) cc_final: 0.8638 (p0) REVERT: H 40 LYS cc_start: 0.9449 (mmtt) cc_final: 0.9215 (mmmt) REVERT: H 65 ASP cc_start: 0.9295 (t0) cc_final: 0.9053 (t0) REVERT: H 68 GLU cc_start: 0.9190 (tp30) cc_final: 0.8772 (tp30) REVERT: H 90 GLU cc_start: 0.9010 (mp0) cc_final: 0.8727 (mp0) outliers start: 13 outliers final: 11 residues processed: 171 average time/residue: 0.2899 time to fit residues: 67.5754 Evaluate side-chains 173 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 H residue 77 LEU 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: 9.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 90 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.052505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.037626 restraints weight = 75206.473| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.13 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13362 Z= 0.242 Angle : 0.640 10.786 19329 Z= 0.362 Chirality : 0.035 0.181 2229 Planarity : 0.004 0.049 1440 Dihedral : 30.119 116.365 4132 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.82 % Allowed : 25.99 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.29), residues: 840 helix: 2.27 (0.22), residues: 563 sheet: 3.07 (1.22), residues: 21 loop : -0.49 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 25 HIS 0.006 0.001 HIS B 75 PHE 0.006 0.001 PHE B 61 TYR 0.048 0.002 TYR H 80 ARG 0.005 0.000 ARG A 52 ********************** 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: 12 poor density : 157 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8762 (mm-30) REVERT: A 120 MET cc_start: 0.8537 (mtm) cc_final: 0.7703 (mtm) REVERT: D 43 LYS cc_start: 0.9309 (mmtm) cc_final: 0.8940 (tppt) REVERT: D 65 ASP cc_start: 0.9263 (t0) cc_final: 0.8992 (t0) REVERT: D 68 GLU cc_start: 0.9120 (tp30) cc_final: 0.8763 (tp30) REVERT: D 85 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8579 (p) REVERT: D 90 GLU cc_start: 0.8553 (mp0) cc_final: 0.8054 (mp0) REVERT: F 74 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8717 (mm-30) REVERT: F 79 LYS cc_start: 0.9353 (mtmm) cc_final: 0.8686 (mtmm) REVERT: G 39 TYR cc_start: 0.8441 (m-80) cc_final: 0.8109 (m-10) REVERT: H 65 ASP cc_start: 0.9297 (t0) cc_final: 0.8981 (t0) REVERT: H 68 GLU cc_start: 0.9272 (tp30) cc_final: 0.9026 (tp30) REVERT: H 90 GLU cc_start: 0.9022 (mp0) cc_final: 0.8740 (mp0) outliers start: 12 outliers final: 11 residues processed: 165 average time/residue: 0.2941 time to fit residues: 66.2114 Evaluate side-chains 166 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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 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: 9.9990 chunk 93 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.052120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.037317 restraints weight = 75469.252| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.06 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13362 Z= 0.259 Angle : 0.643 9.492 19329 Z= 0.367 Chirality : 0.036 0.180 2229 Planarity : 0.004 0.049 1440 Dihedral : 30.156 115.513 4132 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.98 % Allowed : 26.14 % 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: 2.22 (0.22), residues: 563 sheet: 3.22 (1.22), residues: 21 loop : -0.50 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 25 HIS 0.006 0.001 HIS B 75 PHE 0.005 0.001 PHE C 25 TYR 0.074 0.003 TYR H 80 ARG 0.005 0.000 ARG C 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4372.03 seconds wall clock time: 78 minutes 37.73 seconds (4717.73 seconds total)