Starting phenix.real_space_refine on Wed Jul 1 20:42:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7us9_26729/07_2026/7us9_26729.cif Found real_map, /net/cci-nas-00/data/ceres_data/7us9_26729/07_2026/7us9_26729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7us9_26729/07_2026/7us9_26729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7us9_26729/07_2026/7us9_26729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7us9_26729/07_2026/7us9_26729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7us9_26729/07_2026/7us9_26729.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7us9_26729/07_2026/7us9_26729.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7us9_26729/07_2026/7us9_26729.cif" } resolution = 3.8 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= 0.000 sd= 0.019 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 4 5.16 5 C 744 2.51 5 N 185 2.21 5 O 194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 1127 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1071 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 137} Chain breaks: 7 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 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: "A" 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 Time building chain proxies: 0.36, per 1000 atoms: 0.32 Number of scatterers: 1127 At special positions: 0 Unit cell: (50.58, 48.894, 59.853, 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 4 16.00 O 194 8.00 N 185 7.00 C 744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.09 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-ASN " NAG A 301 " - " ASN A 42 " " NAG A 302 " - " ASN A 242 " " NAG B 1 " - " ASN A 249 " Time building additional restraints: 0.07 Conformation dependent library (CDL) restraints added in 24.6 milliseconds 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 274 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 3 sheets defined 9.7% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 4.150A pdb=" N ILE A 36 " --> pdb=" O HIS A 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 57 Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 7.641A pdb=" N PHE A 202 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LYS A 110 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR A 204 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 109 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR A 112 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 130 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN A 156 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A 132 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 196 removed outlier: 3.514A pdb=" N ALA A 85 " --> pdb=" O VAL A 230 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 141 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: 0.09 Time building geometry restraints manager: 0.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 251 1.33 - 1.46: 358 1.46 - 1.58: 546 1.58 - 1.71: 1 1.71 - 1.84: 6 Bond restraints: 1162 Sorted by residual: bond pdb=" N PRO A 111 " pdb=" CD PRO A 111 " ideal model delta sigma weight residual 1.474 1.381 0.093 1.40e-02 5.10e+03 4.37e+01 bond pdb=" CZ2 TRP A 225 " pdb=" CH2 TRP A 225 " ideal model delta sigma weight residual 1.368 1.455 -0.087 1.90e-02 2.77e+03 2.10e+01 bond pdb=" CD2 TRP A 225 " pdb=" CE3 TRP A 225 " ideal model delta sigma weight residual 1.398 1.468 -0.070 1.60e-02 3.91e+03 1.90e+01 bond pdb=" CB LEU A 76 " pdb=" CG LEU A 76 " ideal model delta sigma weight residual 1.530 1.615 -0.085 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C LEU A 47 " pdb=" N PRO A 48 " ideal model delta sigma weight residual 1.329 1.371 -0.042 1.18e-02 7.18e+03 1.24e+01 ... (remaining 1157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 1429 2.34 - 4.69: 128 4.69 - 7.03: 27 7.03 - 9.38: 3 9.38 - 11.72: 2 Bond angle restraints: 1589 Sorted by residual: angle pdb=" N ILE A 195 " pdb=" CA ILE A 195 " pdb=" C ILE A 195 " ideal model delta sigma weight residual 108.11 117.48 -9.37 1.40e+00 5.10e-01 4.47e+01 angle pdb=" C PHE A 159 " pdb=" N PRO A 160 " pdb=" CA PRO A 160 " ideal model delta sigma weight residual 120.31 126.85 -6.54 9.80e-01 1.04e+00 4.45e+01 angle pdb=" C PRO A 48 " pdb=" N PRO A 49 " pdb=" CA PRO A 49 " ideal model delta sigma weight residual 119.84 127.79 -7.95 1.25e+00 6.40e-01 4.05e+01 angle pdb=" C LEU A 47 " pdb=" N PRO A 48 " pdb=" CA PRO A 48 " ideal model delta sigma weight residual 120.38 126.66 -6.28 1.03e+00 9.43e-01 3.72e+01 angle pdb=" N VAL A 78 " pdb=" CA VAL A 78 " pdb=" CB VAL A 78 " ideal model delta sigma weight residual 110.72 104.39 6.33 1.09e+00 8.42e-01 3.37e+01 ... (remaining 1584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.01: 550 8.01 - 16.02: 37 16.02 - 24.03: 9 24.03 - 32.04: 6 32.04 - 40.05: 2 Dihedral angle restraints: 604 sinusoidal: 182 harmonic: 422 Sorted by residual: dihedral pdb=" C GLN A 63 " pdb=" N GLN A 63 " pdb=" CA GLN A 63 " pdb=" CB GLN A 63 " ideal model delta harmonic sigma weight residual -122.60 -130.32 7.72 0 2.50e+00 1.60e-01 9.54e+00 dihedral pdb=" CA ILE A 195 " pdb=" CB ILE A 195 " pdb=" CG1 ILE A 195 " pdb=" CD1 ILE A 195 " ideal model delta sinusoidal sigma weight residual 60.00 100.05 -40.05 3 1.50e+01 4.44e-03 7.12e+00 dihedral pdb=" C LYS A 110 " pdb=" N LYS A 110 " pdb=" CA LYS A 110 " pdb=" CB LYS A 110 " ideal model delta harmonic sigma weight residual -122.60 -116.09 -6.51 0 2.50e+00 1.60e-01 6.77e+00 ... (remaining 601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 122 0.078 - 0.157: 30 0.157 - 0.235: 13 0.235 - 0.313: 9 0.313 - 0.392: 4 Chirality restraints: 178 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.42e+01 chirality pdb=" C2 NAG B 1 " pdb=" C1 NAG B 1 " pdb=" C3 NAG B 1 " pdb=" N2 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.88 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CG LEU A 76 " pdb=" CB LEU A 76 " pdb=" CD1 LEU A 76 " pdb=" CD2 LEU A 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 175 not shown) Planarity restraints: 196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 42 " -0.046 2.00e-02 2.50e+03 4.80e-02 2.88e+01 pdb=" CG ASN A 42 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 42 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 42 " 0.075 2.00e-02 2.50e+03 pdb=" C1 NAG A 301 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 242 " -0.039 2.00e-02 2.50e+03 4.07e-02 2.07e+01 pdb=" CG ASN A 242 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 242 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 242 " 0.063 2.00e-02 2.50e+03 pdb=" C1 NAG A 302 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 64 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C PRO A 64 " 0.029 2.00e-02 2.50e+03 pdb=" O PRO A 64 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP A 65 " -0.010 2.00e-02 2.50e+03 ... (remaining 193 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 519 2.97 - 3.45: 846 3.45 - 3.94: 1656 3.94 - 4.42: 1735 4.42 - 4.90: 3029 Nonbonded interactions: 7785 Sorted by model distance: nonbonded pdb=" O LYS A 110 " pdb=" CD PRO A 111 " model vdw 2.489 2.752 nonbonded pdb=" O GLN A 178 " pdb=" CA TRP A 179 " model vdw 2.627 2.776 nonbonded pdb=" N GLY A 109 " pdb=" O GLY A 109 " model vdw 2.636 2.496 nonbonded pdb=" N MET A 80 " pdb=" O MET A 80 " model vdw 2.641 2.496 nonbonded pdb=" O HIS A 189 " pdb=" ND1 HIS A 189 " model vdw 2.643 3.120 ... (remaining 7780 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 6.740 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: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.020 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 0.015 0.093 1167 Z= 0.820 Angle : 1.599 11.720 1603 Z= 1.016 Chirality : 0.112 0.392 178 Planarity : 0.005 0.017 193 Dihedral : 7.307 40.047 327 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.07 (0.73), residues: 129 helix: 3.26 (1.42), residues: 12 sheet: 1.80 (0.75), residues: 47 loop : -0.57 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 154 TYR 0.015 0.004 TYR A 43 PHE 0.011 0.003 PHE A 227 TRP 0.015 0.004 TRP A 65 HIS 0.004 0.002 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.01459 / 0.79 ( 1162) covalent geometry : angle 1.58180 / 1.02 ( 1589) SS BOND : bond 0.05691 / 3.00 ( 1) SS BOND : angle 2.69427 / 1.42 ( 2) hydrogen bonds : bond 0.18023 / 13.08 ( 54) hydrogen bonds : angle 7.59859 / 5.71 ( 141) link_BETA1-4 : bond 0.07242 / 3.81 ( 1) link_BETA1-4 : angle 4.52926 / 2.48 ( 3) link_NAG-ASN : bond 0.06837 / 3.42 ( 3) link_NAG-ASN : angle 2.22484 / 2.12 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.040 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0309 time to fit residues: 1.1607 Evaluate side-chains 21 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 13 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 0.0670 chunk 4 optimal weight: 0.1980 chunk 8 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 9 optimal weight: 0.0970 chunk 3 optimal weight: 0.1980 chunk 2 optimal weight: 0.0070 overall best weight: 0.1134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.173733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.153875 restraints weight = 1746.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.156756 restraints weight = 1131.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.158709 restraints weight = 827.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.159908 restraints weight = 656.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.160848 restraints weight = 556.887| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1167 Z= 0.136 Angle : 0.714 7.106 1603 Z= 0.356 Chirality : 0.052 0.217 178 Planarity : 0.004 0.027 193 Dihedral : 4.626 14.528 151 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.47 % Allowed : 9.88 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.39 (0.78), residues: 129 helix: 3.72 (1.25), residues: 12 sheet: 1.47 (0.58), residues: 76 loop : -1.11 (1.10), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 154 TYR 0.007 0.001 TYR A 235 PHE 0.011 0.002 PHE A 59 TRP 0.006 0.001 TRP A 179 HIS 0.001 0.000 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 1162) covalent geometry : angle 0.65084 / 0.34 ( 1589) SS BOND : bond 0.00073 / 0.04 ( 1) SS BOND : angle 1.31991 / 0.72 ( 2) hydrogen bonds : bond 0.04374 / 3.18 ( 54) hydrogen bonds : angle 5.83429 / 4.43 ( 141) link_BETA1-4 : bond 0.00075 / 0.04 ( 1) link_BETA1-4 : angle 1.71737 / 1.04 ( 3) link_NAG-ASN : bond 0.01157 / 0.55 ( 3) link_NAG-ASN : angle 3.81966 / 3.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.026 Fit side-chains REVERT: A 199 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7740 (t0) outliers start: 2 outliers final: 1 residues processed: 23 average time/residue: 0.0218 time to fit residues: 0.6514 Evaluate side-chains 18 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 199 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 0 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.0570 chunk 13 optimal weight: 0.0870 chunk 2 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.0670 overall best weight: 0.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.173282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.150623 restraints weight = 1819.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.153288 restraints weight = 1270.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.154956 restraints weight = 984.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.156150 restraints weight = 822.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.157162 restraints weight = 717.816| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1167 Z= 0.174 Angle : 0.795 10.522 1603 Z= 0.393 Chirality : 0.052 0.152 178 Planarity : 0.006 0.057 193 Dihedral : 4.524 11.901 151 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.70 % Allowed : 8.64 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.77 (0.75), residues: 129 helix: 3.20 (1.26), residues: 12 sheet: 1.04 (0.59), residues: 77 loop : -1.43 (0.97), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 237 TYR 0.007 0.001 TYR A 43 PHE 0.018 0.002 PHE A 197 TRP 0.009 0.001 TRP A 179 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 ( 1162) covalent geometry : angle 0.74569 / 0.38 ( 1589) SS BOND : bond 0.00286 / 0.15 ( 1) SS BOND : angle 1.06513 / 0.57 ( 2) hydrogen bonds : bond 0.04095 / 2.97 ( 54) hydrogen bonds : angle 5.26826 / 4.02 ( 141) link_BETA1-4 : bond 0.00226 / 0.12 ( 1) link_BETA1-4 : angle 1.85108 / 1.16 ( 3) link_NAG-ASN : bond 0.01229 / 0.59 ( 3) link_NAG-ASN : angle 3.59042 / 2.51 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.025 Fit side-chains REVERT: A 80 MET cc_start: 0.7434 (mmm) cc_final: 0.6992 (mmm) REVERT: A 199 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7744 (t0) outliers start: 3 outliers final: 1 residues processed: 17 average time/residue: 0.0153 time to fit residues: 0.3503 Evaluate side-chains 16 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 199 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 13 optimal weight: 0.1980 chunk 0 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.0050 chunk 4 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.169357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146629 restraints weight = 1809.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.149490 restraints weight = 1206.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.151359 restraints weight = 895.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.152158 restraints weight = 730.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.153088 restraints weight = 648.765| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1167 Z= 0.168 Angle : 0.766 10.100 1603 Z= 0.359 Chirality : 0.052 0.175 178 Planarity : 0.006 0.044 193 Dihedral : 4.442 11.181 151 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.23 % Allowed : 11.11 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.44 (0.73), residues: 129 helix: 2.77 (1.25), residues: 12 sheet: 0.83 (0.58), residues: 78 loop : -1.67 (0.90), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 194 TYR 0.009 0.001 TYR A 235 PHE 0.009 0.001 PHE A 59 TRP 0.008 0.001 TRP A 179 HIS 0.001 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 1162) covalent geometry : angle 0.64986 / 0.33 ( 1589) SS BOND : bond 0.00270 / 0.14 ( 1) SS BOND : angle 0.83342 / 0.44 ( 2) hydrogen bonds : bond 0.04067 / 2.92 ( 54) hydrogen bonds : angle 5.04123 / 3.88 ( 141) link_BETA1-4 : bond 0.00032 / 0.02 ( 1) link_BETA1-4 : angle 2.03801 / 1.44 ( 3) link_NAG-ASN : bond 0.00809 / 0.39 ( 3) link_NAG-ASN : angle 5.33143 / 4.99 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.046 Fit side-chains REVERT: A 36 ILE cc_start: 0.9031 (mm) cc_final: 0.8816 (mt) REVERT: A 80 MET cc_start: 0.7524 (mmm) cc_final: 0.7102 (mmm) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.0263 time to fit residues: 0.5654 Evaluate side-chains 13 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 13 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 8 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 overall best weight: 0.2518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.167664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.145761 restraints weight = 1787.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.148029 restraints weight = 1268.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.149726 restraints weight = 992.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.150657 restraints weight = 842.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.151645 restraints weight = 744.225| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1167 Z= 0.182 Angle : 0.839 10.679 1603 Z= 0.415 Chirality : 0.056 0.229 178 Planarity : 0.006 0.039 193 Dihedral : 4.495 13.755 151 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.47 % Allowed : 17.28 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.25 (0.73), residues: 129 helix: 2.92 (1.36), residues: 12 sheet: 0.76 (0.60), residues: 78 loop : -2.03 (0.82), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 194 TYR 0.008 0.001 TYR A 235 PHE 0.030 0.003 PHE A 39 TRP 0.008 0.001 TRP A 179 HIS 0.001 0.000 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 1162) covalent geometry : angle 0.78676 / 0.40 ( 1589) SS BOND : bond 0.00316 / 0.17 ( 1) SS BOND : angle 0.86757 / 0.46 ( 2) hydrogen bonds : bond 0.03949 / 2.81 ( 54) hydrogen bonds : angle 4.90183 / 3.82 ( 141) link_BETA1-4 : bond 0.00032 / 0.02 ( 1) link_BETA1-4 : angle 2.17842 / 1.59 ( 3) link_NAG-ASN : bond 0.00965 / 0.46 ( 3) link_NAG-ASN : angle 3.78904 / 3.01 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.044 Fit side-chains REVERT: A 36 ILE cc_start: 0.9075 (mm) cc_final: 0.8833 (mt) REVERT: A 193 TYR cc_start: 0.7641 (m-80) cc_final: 0.7367 (m-80) outliers start: 2 outliers final: 1 residues processed: 17 average time/residue: 0.0433 time to fit residues: 0.8827 Evaluate side-chains 16 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 13 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.165669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.143479 restraints weight = 1791.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.146028 restraints weight = 1235.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.147555 restraints weight = 955.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.148803 restraints weight = 804.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.149584 restraints weight = 715.609| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 1167 Z= 0.254 Angle : 0.968 15.995 1603 Z= 0.448 Chirality : 0.063 0.451 178 Planarity : 0.007 0.070 193 Dihedral : 5.703 37.871 151 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.47 % Allowed : 18.52 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: -0.39 (0.71), residues: 129 helix: 2.38 (1.35), residues: 12 sheet: 0.46 (0.63), residues: 72 loop : -2.25 (0.68), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 194 TYR 0.013 0.002 TYR A 235 PHE 0.011 0.002 PHE A 202 TRP 0.009 0.002 TRP A 179 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 ( 1162) covalent geometry : angle 0.85094 / 0.42 ( 1589) SS BOND : bond 0.00462 / 0.24 ( 1) SS BOND : angle 0.97186 / 0.52 ( 2) hydrogen bonds : bond 0.04508 / 3.23 ( 54) hydrogen bonds : angle 5.15600 / 4.06 ( 141) link_BETA1-4 : bond 0.00265 / 0.14 ( 1) link_BETA1-4 : angle 2.58458 / 2.09 ( 3) link_NAG-ASN : bond 0.00793 / 0.39 ( 3) link_NAG-ASN : angle 6.06194 / 5.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.041 Fit side-chains REVERT: A 36 ILE cc_start: 0.9175 (mm) cc_final: 0.8945 (mt) REVERT: A 193 TYR cc_start: 0.7666 (m-80) cc_final: 0.7319 (m-80) outliers start: 2 outliers final: 1 residues processed: 16 average time/residue: 0.0687 time to fit residues: 1.2320 Evaluate side-chains 15 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 5 optimal weight: 0.1980 chunk 13 optimal weight: 0.0980 chunk 0 optimal weight: 0.6980 chunk 6 optimal weight: 0.0670 chunk 10 optimal weight: 0.4980 chunk 2 optimal weight: 0.3980 chunk 4 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 9 optimal weight: 0.2980 overall best weight: 0.1118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.170650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.148752 restraints weight = 1747.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.151290 restraints weight = 1195.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.153145 restraints weight = 920.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.154518 restraints weight = 764.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.155296 restraints weight = 662.746| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1167 Z= 0.120 Angle : 0.791 10.239 1603 Z= 0.384 Chirality : 0.065 0.554 178 Planarity : 0.006 0.056 193 Dihedral : 5.438 35.773 151 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.23 % Allowed : 17.28 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: 0.04 (0.74), residues: 129 helix: 4.55 (1.32), residues: 12 sheet: 0.47 (0.63), residues: 74 loop : -2.17 (0.71), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 154 TYR 0.006 0.001 TYR A 43 PHE 0.008 0.001 PHE A 202 TRP 0.007 0.001 TRP A 65 HIS 0.001 0.000 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 1162) covalent geometry : angle 0.70820 / 0.37 ( 1589) SS BOND : bond 0.00152 / 0.08 ( 1) SS BOND : angle 0.71302 / 0.38 ( 2) hydrogen bonds : bond 0.03227 / 2.31 ( 54) hydrogen bonds : angle 4.63700 / 3.62 ( 141) link_BETA1-4 : bond 0.00249 / 0.13 ( 1) link_BETA1-4 : angle 2.26577 / 1.49 ( 3) link_NAG-ASN : bond 0.00444 / 0.22 ( 3) link_NAG-ASN : angle 4.59963 / 3.94 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.041 Fit side-chains REVERT: A 36 ILE cc_start: 0.9034 (mm) cc_final: 0.8731 (mt) REVERT: A 39 PHE cc_start: 0.8934 (t80) cc_final: 0.8688 (t80) REVERT: A 193 TYR cc_start: 0.7586 (m-80) cc_final: 0.7230 (m-80) outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.0587 time to fit residues: 1.4580 Evaluate side-chains 19 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 11 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.0470 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.165327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143533 restraints weight = 1763.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.145948 restraints weight = 1251.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.147426 restraints weight = 978.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.148726 restraints weight = 825.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.149450 restraints weight = 724.722| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 1167 Z= 0.230 Angle : 0.837 9.727 1603 Z= 0.391 Chirality : 0.073 0.700 178 Planarity : 0.006 0.057 193 Dihedral : 5.346 31.939 151 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.47 % Allowed : 18.52 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: -0.43 (0.72), residues: 129 helix: 3.34 (1.25), residues: 12 sheet: 0.34 (0.63), residues: 73 loop : -2.48 (0.68), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 237 TYR 0.012 0.002 TYR A 43 PHE 0.022 0.003 PHE A 197 TRP 0.007 0.001 TRP A 179 HIS 0.002 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 ( 1162) covalent geometry : angle 0.76065 / 0.37 ( 1589) SS BOND : bond 0.00431 / 0.23 ( 1) SS BOND : angle 0.86716 / 0.47 ( 2) hydrogen bonds : bond 0.04374 / 3.12 ( 54) hydrogen bonds : angle 4.93761 / 3.90 ( 141) link_BETA1-4 : bond 0.00393 / 0.21 ( 1) link_BETA1-4 : angle 2.71613 / 2.21 ( 3) link_NAG-ASN : bond 0.00708 / 0.35 ( 3) link_NAG-ASN : angle 4.46581 / 3.77 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.043 Fit side-chains REVERT: A 36 ILE cc_start: 0.9087 (mm) cc_final: 0.8850 (mt) REVERT: A 39 PHE cc_start: 0.9158 (t80) cc_final: 0.8808 (t80) REVERT: A 193 TYR cc_start: 0.7697 (m-80) cc_final: 0.7351 (m-80) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.0565 time to fit residues: 1.5455 Evaluate side-chains 21 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 0 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 5 optimal weight: 0.0980 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 0.0870 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 4 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 11 optimal weight: 0.3980 overall best weight: 0.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.166121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.145913 restraints weight = 1779.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.148458 restraints weight = 1200.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.150271 restraints weight = 919.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.151518 restraints weight = 756.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.152233 restraints weight = 655.591| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1167 Z= 0.148 Angle : 0.771 10.067 1603 Z= 0.363 Chirality : 0.061 0.465 178 Planarity : 0.006 0.053 193 Dihedral : 5.093 32.351 151 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.47 % Allowed : 23.46 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: -0.07 (0.74), residues: 129 helix: 4.19 (1.24), residues: 12 sheet: 0.39 (0.63), residues: 74 loop : -2.13 (0.72), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 237 TYR 0.009 0.001 TYR A 77 PHE 0.020 0.002 PHE A 197 TRP 0.004 0.001 TRP A 179 HIS 0.001 0.000 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 1162) covalent geometry : angle 0.68724 / 0.34 ( 1589) SS BOND : bond 0.00229 / 0.12 ( 1) SS BOND : angle 0.69072 / 0.37 ( 2) hydrogen bonds : bond 0.03524 / 2.45 ( 54) hydrogen bonds : angle 4.66939 / 3.67 ( 141) link_BETA1-4 : bond 0.00084 / 0.04 ( 1) link_BETA1-4 : angle 2.44718 / 1.82 ( 3) link_NAG-ASN : bond 0.00373 / 0.18 ( 3) link_NAG-ASN : angle 4.52640 / 3.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.047 Fit side-chains REVERT: A 36 ILE cc_start: 0.8990 (mm) cc_final: 0.8722 (mt) REVERT: A 39 PHE cc_start: 0.9056 (t80) cc_final: 0.8633 (t80) REVERT: A 193 TYR cc_start: 0.7723 (m-80) cc_final: 0.7406 (m-80) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.0565 time to fit residues: 1.4176 Evaluate side-chains 22 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 240 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 2 optimal weight: 0.0470 chunk 1 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.1980 chunk 12 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 0 optimal weight: 0.0870 chunk 3 optimal weight: 0.0670 chunk 11 optimal weight: 0.2980 chunk 8 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 overall best weight: 0.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.167291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.147206 restraints weight = 1774.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.149943 restraints weight = 1189.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.151624 restraints weight = 900.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.152965 restraints weight = 738.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.153389 restraints weight = 639.821| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 1167 Z= 0.149 Angle : 0.776 8.964 1603 Z= 0.368 Chirality : 0.072 0.664 178 Planarity : 0.006 0.050 193 Dihedral : 5.037 33.250 151 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.47 % Allowed : 20.99 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: 0.07 (0.75), residues: 129 helix: 4.47 (1.23), residues: 12 sheet: 0.35 (0.62), residues: 74 loop : -1.80 (0.80), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 237 TYR 0.007 0.001 TYR A 77 PHE 0.019 0.002 PHE A 197 TRP 0.005 0.001 TRP A 65 HIS 0.001 0.000 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 1162) covalent geometry : angle 0.70245 / 0.35 ( 1589) SS BOND : bond 0.00169 / 0.09 ( 1) SS BOND : angle 0.72471 / 0.38 ( 2) hydrogen bonds : bond 0.03295 / 2.28 ( 54) hydrogen bonds : angle 4.60665 / 3.62 ( 141) link_BETA1-4 : bond 0.00008 / 0.00 ( 1) link_BETA1-4 : angle 2.34347 / 1.74 ( 3) link_NAG-ASN : bond 0.00361 / 0.18 ( 3) link_NAG-ASN : angle 4.27779 / 3.67 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.044 Fit side-chains REVERT: A 36 ILE cc_start: 0.8952 (mm) cc_final: 0.8675 (mt) REVERT: A 39 PHE cc_start: 0.9049 (t80) cc_final: 0.8616 (t80) REVERT: A 193 TYR cc_start: 0.7720 (m-80) cc_final: 0.7392 (m-80) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.0600 time to fit residues: 1.4936 Evaluate side-chains 22 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 240 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 13 optimal weight: 0.2980 chunk 1 optimal weight: 0.0870 chunk 3 optimal weight: 0.3980 chunk 8 optimal weight: 0.4980 chunk 6 optimal weight: 0.0870 chunk 0 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 0.0970 overall best weight: 0.1734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.163197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140976 restraints weight = 1812.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.143792 restraints weight = 1179.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145654 restraints weight = 888.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.147037 restraints weight = 725.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147824 restraints weight = 627.705| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1167 Z= 0.158 Angle : 0.996 17.478 1603 Z= 0.426 Chirality : 0.119 1.384 178 Planarity : 0.006 0.049 193 Dihedral : 4.994 31.311 151 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.23 % Allowed : 23.46 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: 0.05 (0.74), residues: 129 helix: 4.44 (1.22), residues: 12 sheet: 0.43 (0.62), residues: 74 loop : -2.01 (0.75), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 237 TYR 0.007 0.001 TYR A 77 PHE 0.018 0.002 PHE A 197 TRP 0.004 0.001 TRP A 65 HIS 0.001 0.000 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 1162) covalent geometry : angle 0.83827 / 0.39 ( 1589) SS BOND : bond 0.00222 / 0.12 ( 1) SS BOND : angle 0.70401 / 0.37 ( 2) hydrogen bonds : bond 0.03324 / 2.30 ( 54) hydrogen bonds : angle 4.56304 / 3.59 ( 141) link_BETA1-4 : bond 0.00001 / 0.00 ( 1) link_BETA1-4 : angle 2.39607 / 1.81 ( 3) link_NAG-ASN : bond 0.00304 / 0.15 ( 3) link_NAG-ASN : angle 7.10392 / 6.10 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 694.39 seconds wall clock time: 12 minutes 46.63 seconds (766.63 seconds total)