Starting phenix.real_space_refine on Thu Jul 2 00:04:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uaq_26430/07_2026/7uaq_26430.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uaq_26430/07_2026/7uaq_26430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uaq_26430/07_2026/7uaq_26430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uaq_26430/07_2026/7uaq_26430.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uaq_26430/07_2026/7uaq_26430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uaq_26430/07_2026/7uaq_26430.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7uaq_26430/07_2026/7uaq_26430.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uaq_26430/07_2026/7uaq_26430.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.003 sd= 0.035 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: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2773 2.51 5 N 723 2.21 5 O 850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4362 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2392 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain breaks: 2 Chain: "H" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 833 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.08, per 1000 atoms: 0.25 Number of scatterers: 4362 At special positions: 0 Unit cell: (96.82, 64.89, 89.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 850 8.00 N 723 7.00 C 2773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG B 1 " - " ASN A 122 " " NAG C 1 " - " ASN A 149 " " NAG D 1 " - " ASN A 234 " " NAG L 301 " - " ASN L 20 " Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 177.2 milliseconds 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 12 sheets defined 4.9% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.625A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 29 removed outlier: 3.625A pdb=" N ASN L 29 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.628A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.319A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.501A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.301A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.693A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 7 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 34 through 39 removed outlier: 7.162A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 88 through 89 removed outlier: 3.612A pdb=" N ALA H 88 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 93 through 95 removed outlier: 3.936A pdb=" N ILE H 112 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.524A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER L 67 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 44 through 50 removed outlier: 6.653A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) 91 hydrogen bonds defined for protein. 231 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: 0.67 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1293 1.34 - 1.46: 1224 1.46 - 1.59: 1933 1.59 - 1.72: 0 1.72 - 1.84: 22 Bond restraints: 4472 Sorted by residual: bond pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.02e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" N ILE A 197 " pdb=" CA ILE A 197 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.18e-02 7.18e+03 8.87e+00 bond pdb=" N ILE A 68 " pdb=" CA ILE A 68 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.85e+00 bond pdb=" N GLY L 101 " pdb=" CA GLY L 101 " ideal model delta sigma weight residual 1.447 1.474 -0.027 1.09e-02 8.42e+03 6.11e+00 ... (remaining 4467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 5766 2.49 - 4.99: 266 4.99 - 7.48: 28 7.48 - 9.98: 11 9.98 - 12.47: 2 Bond angle restraints: 6073 Sorted by residual: angle pdb=" C ASN A 165 " pdb=" CA ASN A 165 " pdb=" CB ASN A 165 " ideal model delta sigma weight residual 110.42 122.89 -12.47 1.99e+00 2.53e-01 3.93e+01 angle pdb=" N ASN A 122 " pdb=" CA ASN A 122 " pdb=" CB ASN A 122 " ideal model delta sigma weight residual 110.45 101.66 8.79 1.44e+00 4.82e-01 3.73e+01 angle pdb=" CA GLY L 101 " pdb=" C GLY L 101 " pdb=" O GLY L 101 " ideal model delta sigma weight residual 122.29 117.98 4.31 8.10e-01 1.52e+00 2.83e+01 angle pdb=" N ASN A 165 " pdb=" CA ASN A 165 " pdb=" CB ASN A 165 " ideal model delta sigma weight residual 110.49 101.68 8.81 1.69e+00 3.50e-01 2.72e+01 angle pdb=" N ASN L 20 " pdb=" CA ASN L 20 " pdb=" CB ASN L 20 " ideal model delta sigma weight residual 110.84 104.20 6.64 1.52e+00 4.33e-01 1.91e+01 ... (remaining 6068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.78: 2252 14.78 - 29.56: 210 29.56 - 44.34: 47 44.34 - 59.13: 16 59.13 - 73.91: 4 Dihedral angle restraints: 2529 sinusoidal: 987 harmonic: 1542 Sorted by residual: dihedral pdb=" N ASN A 122 " pdb=" C ASN A 122 " pdb=" CA ASN A 122 " pdb=" CB ASN A 122 " ideal model delta harmonic sigma weight residual 122.80 110.48 12.32 0 2.50e+00 1.60e-01 2.43e+01 dihedral pdb=" CA GLN H 81 " pdb=" C GLN H 81 " pdb=" N MET H 82 " pdb=" CA MET H 82 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA HIS L 54B" pdb=" C HIS L 54B" pdb=" N THR L 54C" pdb=" CA THR L 54C" ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 2526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 537 0.078 - 0.155: 128 0.155 - 0.233: 15 0.233 - 0.310: 3 0.310 - 0.388: 4 Chirality restraints: 687 Sorted by residual: chirality pdb=" C4 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C5 NAG C 1 " pdb=" O4 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.14 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 149 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 684 not shown) Planarity restraints: 773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " 0.010 2.00e-02 2.50e+03 7.50e-02 7.02e+01 pdb=" CG ASN A 165 " -0.093 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.089 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 224 " 0.085 5.00e-02 4.00e+02 1.29e-01 2.64e+01 pdb=" N PRO A 225 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO A 225 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 225 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " 0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" CG ASN A 165 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " 0.026 2.00e-02 2.50e+03 ... (remaining 770 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 125 2.66 - 3.22: 4192 3.22 - 3.78: 6567 3.78 - 4.34: 9038 4.34 - 4.90: 14761 Nonbonded interactions: 34683 Sorted by model distance: nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 102 " model vdw 2.101 3.040 nonbonded pdb=" OG1 THR L 22 " pdb=" OE2 GLU L 70 " model vdw 2.102 3.040 nonbonded pdb=" OE2 GLU A 96 " pdb=" N ASN A 99 " model vdw 2.158 3.120 nonbonded pdb=" O SER H 30 " pdb=" OG1 THR H 52A" model vdw 2.174 3.040 nonbonded pdb=" OE1 GLN A 14 " pdb=" NH1 ARG A 158 " model vdw 2.210 3.120 ... (remaining 34678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.540 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 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 : 0.006 0.061 4487 Z= 0.326 Angle : 1.297 20.097 6113 Z= 0.686 Chirality : 0.071 0.388 687 Planarity : 0.008 0.129 766 Dihedral : 12.787 73.906 1530 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 25.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Rotamer: Outliers : 0.22 % Allowed : 0.86 % Favored : 98.92 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.35), residues: 523 helix: -0.03 (1.56), residues: 11 sheet: -0.76 (0.46), residues: 139 loop : -2.30 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 319 TYR 0.032 0.002 TYR A 144 PHE 0.032 0.003 PHE L 72 TRP 0.020 0.002 TRP A 152 HIS 0.008 0.002 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.32 ( 4472) covalent geometry : angle 1.18662 / 0.66 ( 6073) SS BOND : bond 0.00625 / 0.35 ( 5) SS BOND : angle 3.78987 / 2.14 ( 10) hydrogen bonds : bond 0.28573 / 19.01 ( 89) hydrogen bonds : angle 10.97881 / 7.17 ( 231) link_BETA1-4 : bond 0.00514 / 0.25 ( 3) link_BETA1-4 : angle 1.66685 / 1.00 ( 9) link_NAG-ASN : bond 0.01575 / 0.81 ( 7) link_NAG-ASN : angle 8.64520 / 5.49 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8280 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 158 ARG cc_start: 0.8273 (mtt-85) cc_final: 0.8067 (mtt-85) REVERT: A 211 ASN cc_start: 0.8320 (p0) cc_final: 0.8032 (p0) REVERT: A 314 GLN cc_start: 0.6398 (tp40) cc_final: 0.6067 (tp40) REVERT: H 38 ARG cc_start: 0.6298 (ttm-80) cc_final: 0.6051 (ttm-80) REVERT: H 67 PHE cc_start: 0.7819 (m-80) cc_final: 0.7310 (m-80) REVERT: H 97 TYR cc_start: 0.7891 (t80) cc_final: 0.7566 (t80) REVERT: L 72 PHE cc_start: 0.7263 (m-10) cc_final: 0.6951 (m-80) outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.0596 time to fit residues: 10.1316 Evaluate side-chains 87 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.118624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.094674 restraints weight = 10918.055| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 5.03 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4487 Z= 0.196 Angle : 0.934 12.128 6113 Z= 0.454 Chirality : 0.054 0.355 687 Planarity : 0.006 0.066 766 Dihedral : 5.703 25.281 584 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 2.59 % Allowed : 12.53 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.34), residues: 523 helix: 0.87 (1.69), residues: 11 sheet: -0.59 (0.45), residues: 137 loop : -2.24 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 38 TYR 0.025 0.002 TYR H 50 PHE 0.024 0.002 PHE A 238 TRP 0.012 0.002 TRP H 113 HIS 0.007 0.002 HIS H 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 ( 4472) covalent geometry : angle 0.86954 / 0.44 ( 6073) SS BOND : bond 0.00926 / 0.47 ( 5) SS BOND : angle 2.31675 / 1.23 ( 10) hydrogen bonds : bond 0.04001 / 2.61 ( 89) hydrogen bonds : angle 7.00818 / 4.73 ( 231) link_BETA1-4 : bond 0.00731 / 0.35 ( 3) link_BETA1-4 : angle 1.45179 / 0.85 ( 9) link_NAG-ASN : bond 0.01298 / 0.62 ( 7) link_NAG-ASN : angle 5.63451 / 3.40 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8205 (tm-30) REVERT: A 190 ARG cc_start: 0.8045 (mtt-85) cc_final: 0.7484 (mtt-85) REVERT: A 211 ASN cc_start: 0.8672 (p0) cc_final: 0.8425 (p0) REVERT: A 298 GLU cc_start: 0.6957 (pt0) cc_final: 0.6198 (pt0) REVERT: A 314 GLN cc_start: 0.6769 (tp40) cc_final: 0.6267 (tp40) REVERT: H 105 TYR cc_start: 0.6520 (m-10) cc_final: 0.6079 (m-10) REVERT: L 4 LEU cc_start: 0.7533 (pt) cc_final: 0.7156 (pt) REVERT: L 85 ASP cc_start: 0.7597 (m-30) cc_final: 0.6972 (m-30) outliers start: 12 outliers final: 9 residues processed: 103 average time/residue: 0.0711 time to fit residues: 9.2825 Evaluate side-chains 98 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.116315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.092263 restraints weight = 10843.566| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 5.01 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4487 Z= 0.171 Angle : 0.850 12.231 6113 Z= 0.411 Chirality : 0.051 0.335 687 Planarity : 0.005 0.050 766 Dihedral : 5.380 23.880 582 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 3.24 % Allowed : 14.25 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.35), residues: 523 helix: 1.33 (1.85), residues: 11 sheet: -0.49 (0.43), residues: 147 loop : -2.17 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 103 TYR 0.021 0.002 TYR H 50 PHE 0.020 0.002 PHE A 238 TRP 0.009 0.002 TRP L 91 HIS 0.005 0.001 HIS H 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 4472) covalent geometry : angle 0.78584 / 0.40 ( 6073) SS BOND : bond 0.00336 / 0.17 ( 5) SS BOND : angle 1.89073 / 1.05 ( 10) hydrogen bonds : bond 0.03527 / 2.23 ( 89) hydrogen bonds : angle 6.41204 / 4.37 ( 231) link_BETA1-4 : bond 0.00437 / 0.21 ( 3) link_BETA1-4 : angle 1.36280 / 0.77 ( 9) link_NAG-ASN : bond 0.01136 / 0.56 ( 7) link_NAG-ASN : angle 5.38466 / 3.24 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8196 (tm-30) REVERT: A 132 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7338 (tm-30) REVERT: A 190 ARG cc_start: 0.8042 (mtt-85) cc_final: 0.7515 (mtt-85) REVERT: A 298 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6101 (pt0) REVERT: A 314 GLN cc_start: 0.6881 (tp40) cc_final: 0.6607 (tp40) REVERT: H 57 ARG cc_start: 0.8380 (mmt-90) cc_final: 0.8127 (mmt-90) REVERT: H 94 ARG cc_start: 0.8705 (tmm160) cc_final: 0.8483 (tmm-80) REVERT: L 4 LEU cc_start: 0.7553 (pt) cc_final: 0.7199 (pt) REVERT: L 70 GLU cc_start: 0.7839 (pp20) cc_final: 0.6939 (pp20) REVERT: L 85 ASP cc_start: 0.7733 (m-30) cc_final: 0.7531 (m-30) outliers start: 15 outliers final: 9 residues processed: 102 average time/residue: 0.0804 time to fit residues: 10.2555 Evaluate side-chains 100 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 0.0000 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 47 optimal weight: 0.0010 chunk 23 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.117537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.093334 restraints weight = 10619.309| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 5.03 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4487 Z= 0.139 Angle : 0.784 11.388 6113 Z= 0.378 Chirality : 0.050 0.330 687 Planarity : 0.005 0.049 766 Dihedral : 5.140 22.929 582 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 4.54 % Allowed : 14.69 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.35), residues: 523 helix: 1.38 (1.88), residues: 11 sheet: -0.41 (0.44), residues: 147 loop : -2.09 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 103 TYR 0.020 0.002 TYR H 50 PHE 0.014 0.002 PHE A 238 TRP 0.015 0.002 TRP H 36 HIS 0.006 0.001 HIS H 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 4472) covalent geometry : angle 0.72034 / 0.36 ( 6073) SS BOND : bond 0.00314 / 0.17 ( 5) SS BOND : angle 1.59209 / 0.89 ( 10) hydrogen bonds : bond 0.03172 / 2.02 ( 89) hydrogen bonds : angle 6.15847 / 4.22 ( 231) link_BETA1-4 : bond 0.00514 / 0.25 ( 3) link_BETA1-4 : angle 1.24228 / 0.69 ( 9) link_NAG-ASN : bond 0.01117 / 0.54 ( 7) link_NAG-ASN : angle 5.19151 / 3.12 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8167 (tm-30) REVERT: A 132 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7555 (tm-30) REVERT: A 153 MET cc_start: 0.7188 (ptt) cc_final: 0.6580 (ptt) REVERT: A 190 ARG cc_start: 0.8008 (mtt-85) cc_final: 0.7580 (mtt-85) REVERT: A 298 GLU cc_start: 0.7008 (pt0) cc_final: 0.6141 (pt0) REVERT: A 314 GLN cc_start: 0.6846 (tp40) cc_final: 0.6571 (tp40) REVERT: L 4 LEU cc_start: 0.7492 (pt) cc_final: 0.7157 (pt) REVERT: L 42 LYS cc_start: 0.8510 (mppt) cc_final: 0.8021 (mmtm) REVERT: L 45 ARG cc_start: 0.7315 (mtm110) cc_final: 0.7004 (ttp-110) REVERT: L 70 GLU cc_start: 0.7914 (pp20) cc_final: 0.7287 (pp20) REVERT: L 103 ARG cc_start: 0.8601 (mmm160) cc_final: 0.7889 (tpp-160) outliers start: 21 outliers final: 16 residues processed: 111 average time/residue: 0.0709 time to fit residues: 9.9353 Evaluate side-chains 108 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.115387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.090915 restraints weight = 10919.616| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 5.09 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4487 Z= 0.166 Angle : 0.776 10.597 6113 Z= 0.374 Chirality : 0.049 0.338 687 Planarity : 0.005 0.047 766 Dihedral : 5.098 22.292 582 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 4.32 % Allowed : 15.55 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.36), residues: 523 helix: 1.41 (1.87), residues: 11 sheet: -0.41 (0.45), residues: 147 loop : -1.96 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.020 0.002 TYR H 50 PHE 0.014 0.001 PHE A 238 TRP 0.009 0.001 TRP A 258 HIS 0.005 0.001 HIS H 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 4472) covalent geometry : angle 0.71525 / 0.36 ( 6073) SS BOND : bond 0.00349 / 0.19 ( 5) SS BOND : angle 1.51303 / 0.86 ( 10) hydrogen bonds : bond 0.03046 / 1.91 ( 89) hydrogen bonds : angle 6.05210 / 4.15 ( 231) link_BETA1-4 : bond 0.00576 / 0.28 ( 3) link_BETA1-4 : angle 1.30351 / 0.72 ( 9) link_NAG-ASN : bond 0.01036 / 0.51 ( 7) link_NAG-ASN : angle 5.03621 / 3.04 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 115 GLN cc_start: 0.8781 (mm110) cc_final: 0.8539 (mm-40) REVERT: A 132 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7634 (tm-30) REVERT: A 190 ARG cc_start: 0.7952 (mtt-85) cc_final: 0.7596 (mtt-85) REVERT: A 314 GLN cc_start: 0.6935 (tp40) cc_final: 0.6643 (tp40) REVERT: H 57 ARG cc_start: 0.8317 (mmt-90) cc_final: 0.7901 (mmt-90) REVERT: L 4 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7266 (pt) REVERT: L 42 LYS cc_start: 0.8464 (mppt) cc_final: 0.7961 (mmtm) REVERT: L 45 ARG cc_start: 0.7418 (mtm110) cc_final: 0.7130 (ttp-110) REVERT: L 70 GLU cc_start: 0.7944 (pp20) cc_final: 0.7364 (pp20) REVERT: L 103 ARG cc_start: 0.8612 (mmm160) cc_final: 0.8223 (mmm160) outliers start: 20 outliers final: 16 residues processed: 104 average time/residue: 0.0670 time to fit residues: 8.7221 Evaluate side-chains 108 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.111951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.087232 restraints weight = 11056.065| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 5.10 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4487 Z= 0.204 Angle : 0.787 9.951 6113 Z= 0.383 Chirality : 0.049 0.285 687 Planarity : 0.005 0.047 766 Dihedral : 5.299 21.642 582 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.94 % Favored : 89.87 % Rotamer: Outliers : 5.62 % Allowed : 16.63 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.36), residues: 523 helix: 1.62 (1.91), residues: 11 sheet: -0.58 (0.45), residues: 147 loop : -1.92 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.019 0.002 TYR H 50 PHE 0.013 0.002 PHE A 238 TRP 0.016 0.002 TRP A 258 HIS 0.005 0.002 HIS H 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 4472) covalent geometry : angle 0.72914 / 0.37 ( 6073) SS BOND : bond 0.00243 / 0.13 ( 5) SS BOND : angle 1.84026 / 1.01 ( 10) hydrogen bonds : bond 0.03116 / 2.00 ( 89) hydrogen bonds : angle 6.19008 / 4.20 ( 231) link_BETA1-4 : bond 0.00469 / 0.23 ( 3) link_BETA1-4 : angle 1.35646 / 0.75 ( 9) link_NAG-ASN : bond 0.00995 / 0.51 ( 7) link_NAG-ASN : angle 4.91444 / 2.98 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8130 (tm-30) REVERT: A 115 GLN cc_start: 0.8829 (mm110) cc_final: 0.8573 (mm-40) REVERT: A 132 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7740 (tm-30) REVERT: A 190 ARG cc_start: 0.7985 (mtt-85) cc_final: 0.7594 (mtt-85) REVERT: A 314 GLN cc_start: 0.7145 (tp40) cc_final: 0.6874 (tp40) REVERT: H 38 ARG cc_start: 0.8381 (ttp80) cc_final: 0.8137 (ttp80) REVERT: H 57 ARG cc_start: 0.8394 (mmt-90) cc_final: 0.7929 (mmt-90) REVERT: H 100 TYR cc_start: 0.9342 (m-80) cc_final: 0.9058 (m-80) REVERT: L 4 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7370 (pt) REVERT: L 45 ARG cc_start: 0.7585 (mtm110) cc_final: 0.7316 (ttp-110) REVERT: L 70 GLU cc_start: 0.8019 (pp20) cc_final: 0.7310 (pp20) REVERT: L 103 ARG cc_start: 0.8543 (mmm160) cc_final: 0.8319 (mmm160) outliers start: 26 outliers final: 19 residues processed: 105 average time/residue: 0.0680 time to fit residues: 9.0827 Evaluate side-chains 107 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 0.0020 chunk 38 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.110865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.086097 restraints weight = 10850.846| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 5.06 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4487 Z= 0.202 Angle : 0.791 9.950 6113 Z= 0.387 Chirality : 0.050 0.360 687 Planarity : 0.005 0.048 766 Dihedral : 5.321 22.044 582 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.56 % Favored : 90.25 % Rotamer: Outliers : 4.97 % Allowed : 18.36 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.36), residues: 523 helix: 1.63 (1.92), residues: 11 sheet: -0.68 (0.44), residues: 153 loop : -1.94 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.020 0.002 TYR H 50 PHE 0.012 0.002 PHE A 238 TRP 0.012 0.002 TRP A 258 HIS 0.005 0.002 HIS H 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 4472) covalent geometry : angle 0.73655 / 0.37 ( 6073) SS BOND : bond 0.00229 / 0.13 ( 5) SS BOND : angle 1.92144 / 1.01 ( 10) hydrogen bonds : bond 0.03052 / 1.94 ( 89) hydrogen bonds : angle 6.26947 / 4.25 ( 231) link_BETA1-4 : bond 0.00404 / 0.20 ( 3) link_BETA1-4 : angle 1.31609 / 0.72 ( 9) link_NAG-ASN : bond 0.00971 / 0.50 ( 7) link_NAG-ASN : angle 4.75812 / 2.90 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8194 (tm-30) REVERT: A 115 GLN cc_start: 0.8936 (mm110) cc_final: 0.8670 (mm-40) REVERT: A 173 GLN cc_start: 0.8567 (tp40) cc_final: 0.8143 (tp40) REVERT: A 190 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7598 (mtt-85) REVERT: A 314 GLN cc_start: 0.7163 (tp40) cc_final: 0.6914 (tp40) REVERT: H 38 ARG cc_start: 0.8361 (ttp80) cc_final: 0.8127 (ttp80) REVERT: H 57 ARG cc_start: 0.8407 (mmt-90) cc_final: 0.7960 (mmt-90) REVERT: H 100 TYR cc_start: 0.9336 (m-80) cc_final: 0.9132 (m-80) REVERT: L 4 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7367 (pt) REVERT: L 45 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7354 (ttp-110) REVERT: L 70 GLU cc_start: 0.8195 (pp20) cc_final: 0.7551 (pp20) REVERT: L 103 ARG cc_start: 0.8439 (mmm160) cc_final: 0.8176 (mmm160) outliers start: 23 outliers final: 19 residues processed: 106 average time/residue: 0.0661 time to fit residues: 8.8570 Evaluate side-chains 112 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.112241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.087625 restraints weight = 10842.455| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 5.11 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4487 Z= 0.153 Angle : 0.789 10.262 6113 Z= 0.379 Chirality : 0.049 0.328 687 Planarity : 0.005 0.049 766 Dihedral : 5.214 21.007 582 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.33 % Favored : 89.48 % Rotamer: Outliers : 4.54 % Allowed : 20.30 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.36), residues: 523 helix: 1.70 (1.93), residues: 11 sheet: -0.60 (0.44), residues: 153 loop : -1.90 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.024 0.002 TYR H 105 PHE 0.011 0.001 PHE A 318 TRP 0.012 0.001 TRP H 36 HIS 0.005 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 4472) covalent geometry : angle 0.73902 / 0.37 ( 6073) SS BOND : bond 0.00214 / 0.12 ( 5) SS BOND : angle 1.09508 / 0.62 ( 10) hydrogen bonds : bond 0.02872 / 1.85 ( 89) hydrogen bonds : angle 6.11075 / 4.14 ( 231) link_BETA1-4 : bond 0.00526 / 0.26 ( 3) link_BETA1-4 : angle 1.26712 / 0.69 ( 9) link_NAG-ASN : bond 0.00946 / 0.48 ( 7) link_NAG-ASN : angle 4.67003 / 2.85 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 115 GLN cc_start: 0.8929 (mm110) cc_final: 0.8668 (mm-40) REVERT: A 173 GLN cc_start: 0.8564 (tp40) cc_final: 0.8169 (tp40) REVERT: A 190 ARG cc_start: 0.8163 (mtt-85) cc_final: 0.7567 (mtt-85) REVERT: A 314 GLN cc_start: 0.7105 (tp40) cc_final: 0.6852 (tp40) REVERT: H 38 ARG cc_start: 0.8324 (ttp80) cc_final: 0.7979 (ttp80) REVERT: H 57 ARG cc_start: 0.8420 (mmt-90) cc_final: 0.7973 (mmt-90) REVERT: H 72 ASP cc_start: 0.8183 (p0) cc_final: 0.7703 (p0) REVERT: H 76 ASN cc_start: 0.7722 (t0) cc_final: 0.7459 (t0) REVERT: L 4 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7208 (pt) REVERT: L 45 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7379 (ttp-110) REVERT: L 70 GLU cc_start: 0.8143 (pp20) cc_final: 0.7545 (pp20) outliers start: 21 outliers final: 14 residues processed: 105 average time/residue: 0.0612 time to fit residues: 8.0926 Evaluate side-chains 111 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 0.0020 chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.111197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.086629 restraints weight = 10932.657| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 5.06 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4487 Z= 0.179 Angle : 0.803 9.770 6113 Z= 0.390 Chirality : 0.050 0.347 687 Planarity : 0.005 0.049 766 Dihedral : 5.214 20.400 582 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 3.89 % Allowed : 21.38 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.36), residues: 523 helix: 1.68 (1.94), residues: 11 sheet: -0.65 (0.43), residues: 155 loop : -1.91 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 103 TYR 0.017 0.002 TYR H 50 PHE 0.010 0.001 PHE A 318 TRP 0.011 0.001 TRP A 258 HIS 0.005 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 4472) covalent geometry : angle 0.75724 / 0.38 ( 6073) SS BOND : bond 0.00212 / 0.11 ( 5) SS BOND : angle 1.00360 / 0.56 ( 10) hydrogen bonds : bond 0.02829 / 1.80 ( 89) hydrogen bonds : angle 6.19090 / 4.17 ( 231) link_BETA1-4 : bond 0.00489 / 0.24 ( 3) link_BETA1-4 : angle 1.21236 / 0.65 ( 9) link_NAG-ASN : bond 0.00917 / 0.47 ( 7) link_NAG-ASN : angle 4.57763 / 2.80 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8241 (tm-30) REVERT: A 173 GLN cc_start: 0.8602 (tp40) cc_final: 0.8201 (tp40) REVERT: A 190 ARG cc_start: 0.8179 (mtt-85) cc_final: 0.7550 (mtt-85) REVERT: A 314 GLN cc_start: 0.7139 (tp40) cc_final: 0.6909 (tp40) REVERT: H 38 ARG cc_start: 0.8277 (ttp80) cc_final: 0.8054 (ttp80) REVERT: H 57 ARG cc_start: 0.8433 (mmt-90) cc_final: 0.8016 (mmt-90) REVERT: H 72 ASP cc_start: 0.8065 (p0) cc_final: 0.7697 (p0) REVERT: H 76 ASN cc_start: 0.7806 (t0) cc_final: 0.7527 (t0) REVERT: H 99 TYR cc_start: 0.9027 (t80) cc_final: 0.8718 (t80) REVERT: L 4 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7168 (pt) REVERT: L 45 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7425 (ttp-110) REVERT: L 70 GLU cc_start: 0.8201 (pp20) cc_final: 0.7536 (pp20) outliers start: 18 outliers final: 15 residues processed: 100 average time/residue: 0.0530 time to fit residues: 6.8537 Evaluate side-chains 113 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.108232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.083396 restraints weight = 10848.546| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 5.04 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 4487 Z= 0.257 Angle : 0.868 9.418 6113 Z= 0.424 Chirality : 0.051 0.341 687 Planarity : 0.005 0.051 766 Dihedral : 5.670 22.175 582 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.47 % Favored : 88.34 % Rotamer: Outliers : 3.67 % Allowed : 22.89 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.35), residues: 523 helix: 1.74 (1.93), residues: 11 sheet: -0.75 (0.42), residues: 156 loop : -1.96 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 103 TYR 0.020 0.002 TYR H 50 PHE 0.012 0.002 PHE A 318 TRP 0.023 0.003 TRP L 91 HIS 0.009 0.002 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.26 ( 4472) covalent geometry : angle 0.82495 / 0.42 ( 6073) SS BOND : bond 0.00305 / 0.16 ( 5) SS BOND : angle 1.17437 / 0.68 ( 10) hydrogen bonds : bond 0.03280 / 2.15 ( 89) hydrogen bonds : angle 6.53954 / 4.38 ( 231) link_BETA1-4 : bond 0.00454 / 0.22 ( 3) link_BETA1-4 : angle 1.26581 / 0.69 ( 9) link_NAG-ASN : bond 0.00912 / 0.48 ( 7) link_NAG-ASN : angle 4.59229 / 2.83 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8152 (tm-30) REVERT: A 115 GLN cc_start: 0.8981 (mm-40) cc_final: 0.8704 (mm-40) REVERT: A 132 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7820 (tm-30) REVERT: A 190 ARG cc_start: 0.8143 (mtt-85) cc_final: 0.7732 (mtt-85) REVERT: A 314 GLN cc_start: 0.7279 (tp40) cc_final: 0.6992 (tp40) REVERT: H 57 ARG cc_start: 0.8402 (mmt-90) cc_final: 0.7998 (mmt-90) REVERT: H 76 ASN cc_start: 0.8093 (t0) cc_final: 0.7745 (t0) REVERT: H 99 TYR cc_start: 0.8999 (t80) cc_final: 0.8678 (t80) REVERT: L 4 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.6990 (pt) REVERT: L 70 GLU cc_start: 0.8236 (pp20) cc_final: 0.7662 (pp20) REVERT: L 82 ASP cc_start: 0.6893 (m-30) cc_final: 0.6487 (m-30) outliers start: 17 outliers final: 15 residues processed: 110 average time/residue: 0.0532 time to fit residues: 7.5754 Evaluate side-chains 111 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 0.6980 chunk 49 optimal weight: 0.0060 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A 183 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.110396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.086240 restraints weight = 10649.991| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 4.92 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4487 Z= 0.153 Angle : 0.826 10.022 6113 Z= 0.405 Chirality : 0.050 0.333 687 Planarity : 0.005 0.050 766 Dihedral : 5.313 21.159 582 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 3.67 % Allowed : 22.89 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.35), residues: 523 helix: 1.55 (1.90), residues: 11 sheet: -0.93 (0.42), residues: 145 loop : -1.85 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.018 0.002 TYR H 50 PHE 0.013 0.001 PHE A 318 TRP 0.019 0.002 TRP L 91 HIS 0.005 0.001 HIS H 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 4472) covalent geometry : angle 0.78512 / 0.40 ( 6073) SS BOND : bond 0.00359 / 0.19 ( 5) SS BOND : angle 0.91160 / 0.51 ( 10) hydrogen bonds : bond 0.02767 / 1.77 ( 89) hydrogen bonds : angle 6.16814 / 4.13 ( 231) link_BETA1-4 : bond 0.00551 / 0.27 ( 3) link_BETA1-4 : angle 1.13231 / 0.61 ( 9) link_NAG-ASN : bond 0.00953 / 0.48 ( 7) link_NAG-ASN : angle 4.41842 / 2.72 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1065.51 seconds wall clock time: 19 minutes 4.19 seconds (1144.19 seconds total)