Starting phenix.real_space_refine on Wed Feb 14 03:24:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/02_2024/7cp9_30421_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/02_2024/7cp9_30421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/02_2024/7cp9_30421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/02_2024/7cp9_30421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/02_2024/7cp9_30421_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/02_2024/7cp9_30421_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 36 5.16 5 C 5572 2.51 5 N 1390 2.21 5 O 1521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 24": "NH1" <-> "NH2" Residue "F PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 79": "NH1" <-> "NH2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G ARG 117": "NH1" <-> "NH2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "H PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 60": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H ARG 117": "NH1" <-> "NH2" Residue "I PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 348": "NH1" <-> "NH2" Residue "J PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 348": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8530 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "B" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 312 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "C" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "D" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "E" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "F" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "G" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 646 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 55 Chain: "H" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 646 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 55 Chain: "I" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2189 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 272} Chain: "J" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2189 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 272} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.34, per 1000 atoms: 0.63 Number of scatterers: 8530 At special positions: 0 Unit cell: (122.694, 140.946, 100.386, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 11 15.00 O 1521 8.00 N 1390 7.00 C 5572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.7 seconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1870 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 2 sheets defined 36.3% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 13 through 45 Proline residue: A 42 - end of helix removed outlier: 4.419A pdb=" N LEU A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 39 removed outlier: 4.086A pdb=" N MET B 20 " --> pdb=" O MET B 16 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'C' and resid 20 through 32 removed outlier: 3.630A pdb=" N ASP C 26 " --> pdb=" O ASP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 Processing helix chain 'D' and resid 20 through 32 removed outlier: 3.631A pdb=" N ASP D 26 " --> pdb=" O ASP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 59 Processing helix chain 'E' and resid 5 through 37 removed outlier: 5.665A pdb=" N ILE E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 49 through 52 Processing helix chain 'F' and resid 5 through 37 removed outlier: 5.664A pdb=" N ILE F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Proline residue: F 29 - end of helix Processing helix chain 'F' and resid 49 through 52 Processing helix chain 'G' and resid 30 through 38 Processing helix chain 'G' and resid 45 through 55 Processing helix chain 'G' and resid 59 through 95 removed outlier: 3.876A pdb=" N ALA G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA G 65 " --> pdb=" O SER G 61 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER G 81 " --> pdb=" O MET G 77 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA G 83 " --> pdb=" O ARG G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 116 Processing helix chain 'H' and resid 30 through 38 Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 59 through 95 removed outlier: 3.876A pdb=" N ALA H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER H 81 " --> pdb=" O MET H 77 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA H 83 " --> pdb=" O ARG H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 116 Processing helix chain 'I' and resid 84 through 91 removed outlier: 3.672A pdb=" N LYS I 91 " --> pdb=" O ARG I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 91 removed outlier: 3.673A pdb=" N LYS J 91 " --> pdb=" O ARG J 88 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'I' and resid 355 through 359 removed outlier: 5.607A pdb=" N GLY I 100 " --> pdb=" O PHE I 356 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU I 358 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS I 102 " --> pdb=" O LEU I 358 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN I 181 " --> pdb=" O PHE I 185 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE I 185 " --> pdb=" O GLN I 181 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU I 282 " --> pdb=" O ALA I 278 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU I 337 " --> pdb=" O LEU I 332 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 355 through 359 removed outlier: 5.607A pdb=" N GLY J 100 " --> pdb=" O PHE J 356 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU J 358 " --> pdb=" O GLY J 100 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS J 102 " --> pdb=" O LEU J 358 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN J 181 " --> pdb=" O PHE J 185 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE J 185 " --> pdb=" O GLN J 181 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE J 323 " --> pdb=" O ASP J 319 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU J 337 " --> pdb=" O LEU J 332 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1554 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1316 1.30 - 1.43: 2165 1.43 - 1.56: 5121 1.56 - 1.68: 23 1.68 - 1.81: 62 Bond restraints: 8687 Sorted by residual: bond pdb=" C31 PC1 E 102 " pdb=" O31 PC1 E 102 " ideal model delta sigma weight residual 1.330 1.402 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C21 PC1 E 102 " pdb=" O21 PC1 E 102 " ideal model delta sigma weight residual 1.331 1.403 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C21 PC1 C 101 " pdb=" O21 PC1 C 101 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C31 PC1 F 102 " pdb=" O31 PC1 F 102 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C31 PC1 G 202 " pdb=" O31 PC1 G 202 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 8682 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.12: 249 107.12 - 113.87: 5162 113.87 - 120.62: 3381 120.62 - 127.37: 2750 127.37 - 134.12: 98 Bond angle restraints: 11640 Sorted by residual: angle pdb=" O12 PC1 C 101 " pdb=" P PC1 C 101 " pdb=" O14 PC1 C 101 " ideal model delta sigma weight residual 123.67 108.98 14.69 3.00e+00 1.11e-01 2.40e+01 angle pdb=" O12 PC1 E 102 " pdb=" P PC1 E 102 " pdb=" O14 PC1 E 102 " ideal model delta sigma weight residual 123.67 108.99 14.68 3.00e+00 1.11e-01 2.39e+01 angle pdb=" O12 PC1 G 201 " pdb=" P PC1 G 201 " pdb=" O14 PC1 G 201 " ideal model delta sigma weight residual 123.67 109.09 14.58 3.00e+00 1.11e-01 2.36e+01 angle pdb=" O12 PC1 G 202 " pdb=" P PC1 G 202 " pdb=" O14 PC1 G 202 " ideal model delta sigma weight residual 123.67 109.22 14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" O12 PC1 F 101 " pdb=" P PC1 F 101 " pdb=" O14 PC1 F 101 " ideal model delta sigma weight residual 123.67 109.23 14.44 3.00e+00 1.11e-01 2.32e+01 ... (remaining 11635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4649 17.61 - 35.21: 437 35.21 - 52.82: 182 52.82 - 70.42: 50 70.42 - 88.03: 21 Dihedral angle restraints: 5339 sinusoidal: 2434 harmonic: 2905 Sorted by residual: dihedral pdb=" CA LYS A 47 " pdb=" C LYS A 47 " pdb=" N LEU A 48 " pdb=" CA LEU A 48 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA LEU A 45 " pdb=" C LEU A 45 " pdb=" N LYS A 46 " pdb=" CA LYS A 46 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP E 41 " pdb=" C ASP E 41 " pdb=" N PRO E 42 " pdb=" CA PRO E 42 " ideal model delta harmonic sigma weight residual -180.00 -160.53 -19.47 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 849 0.038 - 0.075: 289 0.075 - 0.113: 87 0.113 - 0.151: 15 0.151 - 0.189: 1 Chirality restraints: 1241 Sorted by residual: chirality pdb=" CA THR A 41 " pdb=" N THR A 41 " pdb=" C THR A 41 " pdb=" CB THR A 41 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CA ASP I 198 " pdb=" N ASP I 198 " pdb=" C ASP I 198 " pdb=" CB ASP I 198 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ASP J 198 " pdb=" N ASP J 198 " pdb=" C ASP J 198 " pdb=" CB ASP J 198 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 1238 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 41 " 0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO B 42 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 42 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 42 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 332 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO J 333 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO J 333 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 333 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 332 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO I 333 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO I 333 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 333 " -0.027 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 597 2.73 - 3.27: 7928 3.27 - 3.81: 12883 3.81 - 4.36: 15018 4.36 - 4.90: 27533 Nonbonded interactions: 63959 Sorted by model distance: nonbonded pdb=" OH TYR J 221 " pdb=" OE1 GLN J 223 " model vdw 2.183 2.440 nonbonded pdb=" OH TYR I 221 " pdb=" OE1 GLN I 223 " model vdw 2.183 2.440 nonbonded pdb=" OG SER I 122 " pdb=" O ILE I 124 " model vdw 2.263 2.440 nonbonded pdb=" OG SER J 122 " pdb=" O ILE J 124 " model vdw 2.263 2.440 nonbonded pdb=" OD1 ASN C 15 " pdb=" OG1 THR C 17 " model vdw 2.266 2.440 ... (remaining 63954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 47) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 15 through 63) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 29 through 118 or resid 201 through 202)) selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 76 through 361) } 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.090 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.390 Find NCS groups from input model: 0.450 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:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 : 0.007 0.072 8687 Z= 0.473 Angle : 1.241 14.685 11640 Z= 0.522 Chirality : 0.042 0.189 1241 Planarity : 0.004 0.056 1431 Dihedral : 17.402 88.028 3469 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 7.05 % Allowed : 10.04 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.50 (0.25), residues: 997 helix: -0.82 (0.25), residues: 368 sheet: -1.22 (0.25), residues: 380 loop : -3.24 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 57 HIS 0.003 0.001 HIS J 271 PHE 0.017 0.002 PHE A 43 TYR 0.009 0.001 TYR J 275 ARG 0.003 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 258 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ARG cc_start: 0.5327 (OUTLIER) cc_final: 0.4913 (tpp-160) REVERT: C 57 TRP cc_start: 0.5840 (OUTLIER) cc_final: 0.5115 (m100) REVERT: D 57 TRP cc_start: 0.3468 (OUTLIER) cc_final: 0.2925 (t-100) REVERT: F 34 LEU cc_start: 0.9042 (mt) cc_final: 0.8704 (mt) REVERT: G 76 LYS cc_start: 0.7863 (mptm) cc_final: 0.7212 (mmpt) REVERT: G 78 TYR cc_start: 0.8715 (t80) cc_final: 0.8387 (t80) REVERT: H 78 TYR cc_start: 0.8841 (t80) cc_final: 0.8619 (t80) REVERT: H 81 SER cc_start: 0.8942 (t) cc_final: 0.8729 (m) REVERT: H 109 GLU cc_start: 0.7017 (tt0) cc_final: 0.6808 (tt0) REVERT: I 265 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8251 (mm) REVERT: I 297 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8667 (m) REVERT: J 306 ASP cc_start: 0.7594 (p0) cc_final: 0.7253 (p0) outliers start: 59 outliers final: 21 residues processed: 301 average time/residue: 1.1282 time to fit residues: 361.4800 Evaluate side-chains 229 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 203 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 289 GLU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 338 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN H 110 GLN I 163 GLN I 220 HIS I 295 GLN J 163 GLN J 166 HIS J 181 GLN J 189 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8687 Z= 0.303 Angle : 0.728 8.119 11640 Z= 0.366 Chirality : 0.044 0.203 1241 Planarity : 0.005 0.047 1431 Dihedral : 17.139 88.831 1656 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 8.48 % Allowed : 20.91 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.50 (0.27), residues: 997 helix: 0.31 (0.27), residues: 372 sheet: -1.08 (0.25), residues: 396 loop : -2.63 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 57 HIS 0.005 0.001 HIS I 220 PHE 0.024 0.002 PHE G 67 TYR 0.020 0.002 TYR J 221 ARG 0.005 0.001 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 205 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 LYS cc_start: 0.6504 (mmmm) cc_final: 0.6086 (mmtp) REVERT: C 38 ARG cc_start: 0.5076 (OUTLIER) cc_final: 0.4627 (tpp-160) REVERT: D 57 TRP cc_start: 0.3765 (OUTLIER) cc_final: 0.2905 (t-100) REVERT: F 34 LEU cc_start: 0.9062 (mt) cc_final: 0.8720 (mt) REVERT: G 76 LYS cc_start: 0.7857 (mptm) cc_final: 0.7249 (mmtt) REVERT: G 77 MET cc_start: 0.7673 (ptt) cc_final: 0.7414 (ptp) REVERT: G 78 TYR cc_start: 0.8736 (t80) cc_final: 0.8497 (t80) REVERT: H 79 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.6932 (mpt180) REVERT: H 81 SER cc_start: 0.8879 (t) cc_final: 0.8607 (m) REVERT: H 109 GLU cc_start: 0.7076 (tt0) cc_final: 0.6870 (tt0) REVERT: H 117 ARG cc_start: 0.3254 (OUTLIER) cc_final: 0.2732 (tmm-80) REVERT: I 297 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8628 (m) REVERT: I 315 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8349 (mtmm) REVERT: J 114 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7282 (mt0) REVERT: J 306 ASP cc_start: 0.7633 (p0) cc_final: 0.7274 (p0) outliers start: 71 outliers final: 37 residues processed: 248 average time/residue: 1.0619 time to fit residues: 281.3158 Evaluate side-chains 242 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 198 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 117 ARG Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 289 GLU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 338 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 GLN I 220 HIS J 111 ASN J 163 GLN J 181 GLN J 189 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8687 Z= 0.257 Angle : 0.667 8.181 11640 Z= 0.339 Chirality : 0.043 0.190 1241 Planarity : 0.005 0.044 1431 Dihedral : 16.694 87.522 1653 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 9.92 % Allowed : 21.74 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.01 (0.27), residues: 997 helix: 0.80 (0.28), residues: 372 sheet: -0.90 (0.25), residues: 396 loop : -2.42 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 57 HIS 0.005 0.001 HIS J 271 PHE 0.024 0.002 PHE B 31 TYR 0.020 0.002 TYR B 34 ARG 0.006 0.001 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 205 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 LYS cc_start: 0.6474 (mmmm) cc_final: 0.6191 (mptm) REVERT: B 47 LYS cc_start: 0.7943 (tttp) cc_final: 0.5834 (ttpt) REVERT: C 38 ARG cc_start: 0.5258 (OUTLIER) cc_final: 0.4850 (tpp80) REVERT: C 49 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7739 (mp) REVERT: D 57 TRP cc_start: 0.3928 (OUTLIER) cc_final: 0.2772 (t-100) REVERT: F 34 LEU cc_start: 0.9073 (mt) cc_final: 0.8749 (mt) REVERT: G 76 LYS cc_start: 0.7863 (mptm) cc_final: 0.7264 (mmtt) REVERT: G 77 MET cc_start: 0.7693 (ptt) cc_final: 0.7443 (ptp) REVERT: G 78 TYR cc_start: 0.8750 (t80) cc_final: 0.8487 (t80) REVERT: G 106 LEU cc_start: 0.9045 (tp) cc_final: 0.8699 (tt) REVERT: H 79 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6968 (mpt180) REVERT: H 81 SER cc_start: 0.8884 (t) cc_final: 0.8587 (m) REVERT: H 117 ARG cc_start: 0.3311 (OUTLIER) cc_final: 0.2803 (tmm-80) REVERT: I 297 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8607 (m) REVERT: I 315 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8314 (mtmm) REVERT: J 114 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7295 (mt0) REVERT: J 176 MET cc_start: 0.6292 (mpt) cc_final: 0.6069 (mpt) REVERT: J 180 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8717 (t) REVERT: J 337 LEU cc_start: 0.8629 (tp) cc_final: 0.8422 (mt) outliers start: 83 outliers final: 44 residues processed: 259 average time/residue: 1.0961 time to fit residues: 303.4064 Evaluate side-chains 256 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 203 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 289 GLU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 317 SER Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 77 optimal weight: 0.0000 overall best weight: 1.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS J 163 GLN J 181 GLN J 189 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8687 Z= 0.283 Angle : 0.690 8.741 11640 Z= 0.349 Chirality : 0.043 0.187 1241 Planarity : 0.005 0.044 1431 Dihedral : 16.576 88.538 1652 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 10.27 % Allowed : 23.30 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.27), residues: 997 helix: 0.86 (0.28), residues: 372 sheet: -0.67 (0.26), residues: 398 loop : -2.34 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 57 HIS 0.006 0.001 HIS J 271 PHE 0.031 0.002 PHE G 67 TYR 0.019 0.002 TYR J 275 ARG 0.005 0.000 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 202 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 LYS cc_start: 0.6602 (mmmm) cc_final: 0.6368 (mptm) REVERT: C 38 ARG cc_start: 0.5247 (OUTLIER) cc_final: 0.5010 (ttt180) REVERT: C 49 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7731 (mp) REVERT: F 34 LEU cc_start: 0.9077 (mt) cc_final: 0.8729 (mt) REVERT: G 75 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.7013 (tt0) REVERT: G 76 LYS cc_start: 0.7815 (mptm) cc_final: 0.7217 (mmtt) REVERT: G 77 MET cc_start: 0.7675 (ptt) cc_final: 0.7401 (ptp) REVERT: G 78 TYR cc_start: 0.8770 (t80) cc_final: 0.8508 (t80) REVERT: H 79 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6964 (mpt180) REVERT: H 81 SER cc_start: 0.8892 (t) cc_final: 0.8574 (m) REVERT: H 117 ARG cc_start: 0.3372 (OUTLIER) cc_final: 0.2891 (tmm-80) REVERT: I 123 THR cc_start: 0.9265 (OUTLIER) cc_final: 0.8896 (p) REVERT: I 297 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8593 (m) REVERT: I 315 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8348 (mtmm) REVERT: J 114 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7312 (mt0) REVERT: J 180 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8692 (t) outliers start: 86 outliers final: 47 residues processed: 253 average time/residue: 1.0614 time to fit residues: 286.8036 Evaluate side-chains 257 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 200 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 289 GLU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 0.0050 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS I 295 GLN J 189 GLN J 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8687 Z= 0.241 Angle : 0.679 8.901 11640 Z= 0.339 Chirality : 0.043 0.198 1241 Planarity : 0.004 0.044 1431 Dihedral : 16.120 89.750 1644 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 8.60 % Allowed : 26.16 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.27), residues: 997 helix: 1.05 (0.28), residues: 372 sheet: -0.48 (0.26), residues: 398 loop : -2.25 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 57 HIS 0.005 0.001 HIS J 271 PHE 0.021 0.001 PHE B 31 TYR 0.018 0.002 TYR J 275 ARG 0.007 0.001 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 207 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 38 ARG cc_start: 0.5234 (OUTLIER) cc_final: 0.4765 (tpp80) REVERT: C 43 ARG cc_start: 0.8288 (ptm-80) cc_final: 0.7944 (ppp-140) REVERT: C 49 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7708 (mp) REVERT: F 34 LEU cc_start: 0.9067 (mt) cc_final: 0.8717 (mt) REVERT: G 75 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6910 (tt0) REVERT: G 76 LYS cc_start: 0.7823 (mptm) cc_final: 0.7225 (mmtt) REVERT: G 77 MET cc_start: 0.7596 (ptt) cc_final: 0.7316 (ptp) REVERT: G 78 TYR cc_start: 0.8824 (t80) cc_final: 0.8621 (t80) REVERT: G 79 ARG cc_start: 0.7140 (mpt180) cc_final: 0.6847 (mpt180) REVERT: G 87 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8534 (mp) REVERT: H 79 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6969 (mpt180) REVERT: H 81 SER cc_start: 0.8889 (t) cc_final: 0.8536 (m) REVERT: H 117 ARG cc_start: 0.3571 (OUTLIER) cc_final: 0.3102 (tmm-80) REVERT: I 297 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8454 (m) REVERT: I 315 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8659 (mtmt) REVERT: J 114 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7323 (mt0) REVERT: J 180 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8665 (t) REVERT: J 240 ARG cc_start: 0.6834 (mpp80) cc_final: 0.6540 (mtm180) outliers start: 72 outliers final: 42 residues processed: 250 average time/residue: 1.0345 time to fit residues: 276.6743 Evaluate side-chains 249 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 197 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 289 GLU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS J 189 GLN J 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8687 Z= 0.292 Angle : 0.720 14.602 11640 Z= 0.358 Chirality : 0.044 0.233 1241 Planarity : 0.005 0.046 1431 Dihedral : 16.068 87.188 1643 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 9.32 % Allowed : 27.12 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.28), residues: 997 helix: 0.90 (0.28), residues: 378 sheet: -0.40 (0.26), residues: 398 loop : -2.36 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 57 HIS 0.006 0.001 HIS J 271 PHE 0.026 0.002 PHE B 31 TYR 0.019 0.002 TYR J 275 ARG 0.006 0.001 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 202 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: B 19 LYS cc_start: 0.6689 (mmmm) cc_final: 0.6182 (mmtp) REVERT: C 38 ARG cc_start: 0.5313 (OUTLIER) cc_final: 0.4801 (tpp80) REVERT: C 43 ARG cc_start: 0.8306 (ptm-80) cc_final: 0.8064 (ptm-80) REVERT: C 49 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7715 (mp) REVERT: E 38 ARG cc_start: 0.7203 (ppp80) cc_final: 0.6984 (ptm160) REVERT: F 34 LEU cc_start: 0.9076 (mt) cc_final: 0.8718 (mt) REVERT: G 75 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6857 (tt0) REVERT: G 76 LYS cc_start: 0.7800 (mptm) cc_final: 0.7195 (mmtt) REVERT: G 77 MET cc_start: 0.7616 (ptt) cc_final: 0.7290 (ptp) REVERT: G 78 TYR cc_start: 0.8827 (t80) cc_final: 0.8603 (t80) REVERT: G 79 ARG cc_start: 0.7145 (mpt180) cc_final: 0.6937 (mpt180) REVERT: G 87 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8553 (mp) REVERT: H 79 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7075 (tmt170) REVERT: H 81 SER cc_start: 0.8894 (t) cc_final: 0.8552 (m) REVERT: H 117 ARG cc_start: 0.3529 (OUTLIER) cc_final: 0.3050 (tmm-80) REVERT: I 297 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8538 (m) REVERT: I 315 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8355 (mtmm) REVERT: J 114 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7320 (mt0) REVERT: J 180 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8692 (t) REVERT: J 280 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7677 (m-30) outliers start: 78 outliers final: 48 residues processed: 246 average time/residue: 1.0315 time to fit residues: 271.4274 Evaluate side-chains 258 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 199 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 289 GLU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 287 GLU Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8687 Z= 0.290 Angle : 0.744 19.842 11640 Z= 0.368 Chirality : 0.044 0.199 1241 Planarity : 0.005 0.046 1431 Dihedral : 15.962 85.780 1643 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 8.48 % Allowed : 27.96 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.28), residues: 997 helix: 0.88 (0.27), residues: 380 sheet: -0.38 (0.26), residues: 408 loop : -2.34 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 57 HIS 0.006 0.001 HIS J 271 PHE 0.030 0.002 PHE B 31 TYR 0.020 0.002 TYR J 275 ARG 0.006 0.001 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 199 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 38 ARG cc_start: 0.5397 (OUTLIER) cc_final: 0.4805 (ttm-80) REVERT: C 43 ARG cc_start: 0.8302 (ptm-80) cc_final: 0.8096 (ptm-80) REVERT: C 49 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7721 (mp) REVERT: F 34 LEU cc_start: 0.9085 (mt) cc_final: 0.8735 (mt) REVERT: G 75 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6764 (tt0) REVERT: G 76 LYS cc_start: 0.7784 (mptm) cc_final: 0.7158 (mmtt) REVERT: G 77 MET cc_start: 0.7613 (ptt) cc_final: 0.7302 (ptp) REVERT: G 87 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8559 (mp) REVERT: G 110 GLN cc_start: 0.6843 (tm-30) cc_final: 0.6491 (tt0) REVERT: H 79 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7069 (tmt170) REVERT: H 81 SER cc_start: 0.8895 (t) cc_final: 0.8550 (m) REVERT: H 117 ARG cc_start: 0.3548 (OUTLIER) cc_final: 0.2654 (tmm-80) REVERT: I 297 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8411 (m) REVERT: I 315 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8357 (mtmm) REVERT: I 353 GLN cc_start: 0.7593 (tp40) cc_final: 0.6819 (tp-100) REVERT: J 114 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7325 (mt0) REVERT: J 180 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8693 (t) outliers start: 71 outliers final: 47 residues processed: 238 average time/residue: 1.0522 time to fit residues: 267.4876 Evaluate side-chains 253 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 196 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 289 GLU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 287 GLU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 72 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 75 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8687 Z= 0.216 Angle : 0.729 24.692 11640 Z= 0.355 Chirality : 0.043 0.190 1241 Planarity : 0.004 0.044 1431 Dihedral : 15.591 85.714 1643 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 6.93 % Allowed : 30.35 % Favored : 62.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.28), residues: 997 helix: 1.07 (0.27), residues: 380 sheet: -0.24 (0.27), residues: 398 loop : -2.39 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 57 HIS 0.006 0.001 HIS J 271 PHE 0.026 0.001 PHE B 31 TYR 0.020 0.001 TYR J 275 ARG 0.008 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 198 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 38 ARG cc_start: 0.5323 (OUTLIER) cc_final: 0.4788 (ttm-80) REVERT: C 49 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7730 (mp) REVERT: F 34 LEU cc_start: 0.9046 (mt) cc_final: 0.8716 (mt) REVERT: G 76 LYS cc_start: 0.7781 (mptm) cc_final: 0.7130 (mmtt) REVERT: G 77 MET cc_start: 0.7577 (ptt) cc_final: 0.7320 (ptp) REVERT: G 87 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8525 (mp) REVERT: G 110 GLN cc_start: 0.6834 (tm-30) cc_final: 0.6497 (tt0) REVERT: H 81 SER cc_start: 0.8869 (t) cc_final: 0.8503 (m) REVERT: H 117 ARG cc_start: 0.3453 (OUTLIER) cc_final: 0.3022 (tmm-80) REVERT: I 297 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8286 (m) REVERT: I 315 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8656 (mtmt) REVERT: J 180 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8681 (t) outliers start: 58 outliers final: 37 residues processed: 235 average time/residue: 1.0870 time to fit residues: 273.8524 Evaluate side-chains 234 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 190 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 289 GLU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 287 GLU Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8687 Z= 0.230 Angle : 0.759 28.694 11640 Z= 0.366 Chirality : 0.043 0.216 1241 Planarity : 0.004 0.045 1431 Dihedral : 15.393 86.050 1642 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.85 % Allowed : 31.78 % Favored : 62.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.28), residues: 997 helix: 1.17 (0.27), residues: 378 sheet: -0.11 (0.27), residues: 398 loop : -2.32 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 57 HIS 0.005 0.001 HIS J 271 PHE 0.029 0.001 PHE B 31 TYR 0.021 0.002 TYR J 275 ARG 0.008 0.000 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 196 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: C 49 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7713 (mp) REVERT: F 34 LEU cc_start: 0.9054 (mt) cc_final: 0.8728 (mt) REVERT: G 76 LYS cc_start: 0.7808 (mptm) cc_final: 0.7150 (mmtt) REVERT: G 77 MET cc_start: 0.7591 (ptt) cc_final: 0.7348 (ptp) REVERT: G 87 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8533 (mp) REVERT: H 81 SER cc_start: 0.8870 (t) cc_final: 0.8491 (m) REVERT: H 117 ARG cc_start: 0.3536 (OUTLIER) cc_final: 0.3153 (tmm-80) REVERT: I 297 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8386 (m) REVERT: I 315 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8671 (mtmt) REVERT: J 114 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7339 (mt0) REVERT: J 180 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8672 (t) outliers start: 49 outliers final: 35 residues processed: 228 average time/residue: 1.0786 time to fit residues: 263.3325 Evaluate side-chains 236 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 194 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 289 GLU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 0.0040 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS I 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 8687 Z= 0.220 Angle : 0.796 37.157 11640 Z= 0.378 Chirality : 0.042 0.182 1241 Planarity : 0.004 0.044 1431 Dihedral : 15.163 85.987 1638 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.73 % Allowed : 31.78 % Favored : 62.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.28), residues: 997 helix: 1.28 (0.27), residues: 378 sheet: 0.25 (0.27), residues: 378 loop : -2.34 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 57 HIS 0.006 0.001 HIS I 220 PHE 0.027 0.001 PHE B 31 TYR 0.022 0.001 TYR J 275 ARG 0.007 0.000 ARG D 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 193 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: C 49 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7711 (mp) REVERT: F 34 LEU cc_start: 0.9042 (mt) cc_final: 0.8718 (mt) REVERT: G 76 LYS cc_start: 0.7745 (mptm) cc_final: 0.7070 (mmpt) REVERT: G 77 MET cc_start: 0.7633 (ptt) cc_final: 0.7373 (ptp) REVERT: G 87 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8505 (mp) REVERT: H 81 SER cc_start: 0.8861 (t) cc_final: 0.8479 (m) REVERT: H 105 LYS cc_start: 0.8115 (tmtt) cc_final: 0.7837 (tmtp) REVERT: H 117 ARG cc_start: 0.3606 (OUTLIER) cc_final: 0.3225 (tmm-80) REVERT: I 297 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8394 (m) REVERT: I 315 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8668 (mtmt) REVERT: J 114 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7354 (mt0) REVERT: J 180 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8655 (t) outliers start: 48 outliers final: 31 residues processed: 225 average time/residue: 1.0349 time to fit residues: 249.3231 Evaluate side-chains 226 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 188 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 289 GLU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 126 GLU Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 0.0870 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 0.0770 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 0.0770 chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.183296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.158678 restraints weight = 11725.877| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.87 r_work: 0.3886 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8687 Z= 0.191 Angle : 0.822 44.045 11640 Z= 0.382 Chirality : 0.042 0.179 1241 Planarity : 0.004 0.044 1431 Dihedral : 14.847 86.699 1634 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.30 % Allowed : 33.21 % Favored : 62.49 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.28), residues: 997 helix: 1.44 (0.28), residues: 376 sheet: 0.42 (0.27), residues: 376 loop : -2.11 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 57 HIS 0.004 0.001 HIS J 271 PHE 0.023 0.001 PHE B 31 TYR 0.021 0.001 TYR J 275 ARG 0.007 0.000 ARG D 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4695.12 seconds wall clock time: 83 minutes 20.57 seconds (5000.57 seconds total)