Starting phenix.real_space_refine on Tue Mar 3 10:50:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7us9_26729/03_2026/7us9_26729.cif Found real_map, /net/cci-nas-00/data/ceres_data/7us9_26729/03_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_26729/03_2026/7us9_26729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7us9_26729/03_2026/7us9_26729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7us9_26729/03_2026/7us9_26729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7us9_26729/03_2026/7us9_26729.map" } 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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.50, per 1000 atoms: 0.44 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: 0.09 Conformation dependent library (CDL) restraints added in 28.4 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: 0.06 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: 0.26 Time building geometry restraints manager: 0.12 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: 623 8.01 - 16.02: 44 16.02 - 24.03: 10 24.03 - 32.04: 7 32.04 - 40.05: 4 Dihedral angle restraints: 688 sinusoidal: 266 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 685 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: 4.500 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.610 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 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 : 7.489 40.047 411 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 covalent geometry : bond 0.01459 ( 1162) covalent geometry : angle 1.58180 ( 1589) SS BOND : bond 0.05691 ( 1) SS BOND : angle 2.69427 ( 2) hydrogen bonds : bond 0.18023 ( 54) hydrogen bonds : angle 7.59859 ( 141) link_BETA1-4 : bond 0.07242 ( 1) link_BETA1-4 : angle 4.52926 ( 3) link_NAG-ASN : bond 0.06837 ( 3) link_NAG-ASN : angle 2.22484 ( 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 : 0.024 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0394 time to fit residues: 1.4651 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 : 0.042 ------------------------------------------------------------------------------- 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: 0.2980 chunk 7 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.0070 chunk 2 optimal weight: 0.1980 overall best weight: 0.1536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.172889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.153124 restraints weight = 1767.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.155518 restraints weight = 1182.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.157429 restraints weight = 884.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.158575 restraints weight = 714.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.159532 restraints weight = 614.205| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1167 Z= 0.151 Angle : 0.739 8.115 1603 Z= 0.369 Chirality : 0.052 0.194 178 Planarity : 0.005 0.027 193 Dihedral : 7.745 51.741 235 Min Nonbonded Distance : 2.617 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: 1.37 (0.77), residues: 129 helix: 3.67 (1.28), residues: 12 sheet: 1.49 (0.59), residues: 75 loop : -1.13 (1.05), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 154 TYR 0.008 0.001 TYR A 235 PHE 0.011 0.002 PHE A 59 TRP 0.007 0.001 TRP A 179 HIS 0.001 0.000 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 1162) covalent geometry : angle 0.66928 ( 1589) SS BOND : bond 0.00202 ( 1) SS BOND : angle 1.31018 ( 2) hydrogen bonds : bond 0.04442 ( 54) hydrogen bonds : angle 5.78494 ( 141) link_BETA1-4 : bond 0.00001 ( 1) link_BETA1-4 : angle 1.99983 ( 3) link_NAG-ASN : bond 0.01414 ( 3) link_NAG-ASN : angle 4.07373 ( 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 22 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.027 Fit side-chains REVERT: A 199 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7810 (t0) outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 0.0235 time to fit residues: 0.6889 Evaluate side-chains 15 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.041 ------------------------------------------------------------------------------- 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: 0.9980 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.0060 chunk 13 optimal weight: 0.0770 chunk 2 optimal weight: 0.1980 chunk 9 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.171324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.149403 restraints weight = 1813.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.151750 restraints weight = 1285.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.153184 restraints weight = 1007.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.154506 restraints weight = 849.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155101 restraints weight = 749.955| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3471 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= 0.187 Angle : 0.832 11.880 1603 Z= 0.408 Chirality : 0.053 0.171 178 Planarity : 0.007 0.062 193 Dihedral : 6.928 36.659 235 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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: 0.52 (0.74), residues: 129 helix: 2.67 (1.31), residues: 12 sheet: 0.91 (0.58), residues: 77 loop : -1.57 (0.95), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 237 TYR 0.009 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 covalent geometry : bond 0.00410 ( 1162) covalent geometry : angle 0.75307 ( 1589) SS BOND : bond 0.00340 ( 1) SS BOND : angle 1.19571 ( 2) hydrogen bonds : bond 0.04309 ( 54) hydrogen bonds : angle 5.27401 ( 141) link_BETA1-4 : bond 0.00076 ( 1) link_BETA1-4 : angle 2.03289 ( 3) link_NAG-ASN : bond 0.01271 ( 3) link_NAG-ASN : angle 4.62877 ( 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 17 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.024 Fit side-chains REVERT: A 80 MET cc_start: 0.7485 (mmm) cc_final: 0.7044 (mmm) outliers start: 3 outliers final: 3 residues processed: 16 average time/residue: 0.0193 time to fit residues: 0.4217 Evaluate side-chains 15 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 12 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 177 LEU 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: 2.9990 chunk 5 optimal weight: 0.0970 chunk 6 optimal weight: 0.0870 chunk 3 optimal weight: 0.0470 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 4 optimal weight: 0.0970 chunk 11 optimal weight: 0.3980 overall best weight: 0.0850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.171290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.151125 restraints weight = 1814.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153462 restraints weight = 1190.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.155155 restraints weight = 896.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.156129 restraints weight = 737.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.156603 restraints weight = 642.879| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1167 Z= 0.116 Angle : 0.721 12.129 1603 Z= 0.339 Chirality : 0.054 0.309 178 Planarity : 0.005 0.043 193 Dihedral : 6.333 35.860 235 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.47 % Allowed : 8.64 % Favored : 88.89 % 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: 0.70 (0.74), residues: 129 helix: 3.31 (1.25), residues: 12 sheet: 0.88 (0.59), residues: 78 loop : -1.32 (0.95), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 194 TYR 0.006 0.001 TYR A 236 PHE 0.005 0.001 PHE A 180 TRP 0.005 0.001 TRP A 179 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 1162) covalent geometry : angle 0.59929 ( 1589) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.75830 ( 2) hydrogen bonds : bond 0.03551 ( 54) hydrogen bonds : angle 4.87610 ( 141) link_BETA1-4 : bond 0.00272 ( 1) link_BETA1-4 : angle 2.01412 ( 3) link_NAG-ASN : bond 0.00872 ( 3) link_NAG-ASN : angle 5.26020 ( 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 19 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.025 Fit side-chains REVERT: A 33 TRP cc_start: 0.8400 (t-100) cc_final: 0.8077 (t-100) REVERT: A 36 ILE cc_start: 0.8938 (mm) cc_final: 0.8504 (mt) REVERT: A 80 MET cc_start: 0.7494 (mmm) cc_final: 0.7091 (mmm) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.0200 time to fit residues: 0.4764 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 : 0.033 ------------------------------------------------------------------------------- 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: 0.4980 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 8 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 12 optimal weight: 0.3980 chunk 11 optimal weight: 0.0970 chunk 4 optimal weight: 0.0980 overall best weight: 0.1978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.170074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.148422 restraints weight = 1773.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.150578 restraints weight = 1259.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.152358 restraints weight = 993.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.153437 restraints weight = 842.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.154405 restraints weight = 740.963| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1167 Z= 0.163 Angle : 0.807 10.800 1603 Z= 0.402 Chirality : 0.056 0.229 178 Planarity : 0.006 0.037 193 Dihedral : 7.554 40.406 235 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.23 % Allowed : 14.81 % Favored : 83.95 % 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: 0.52 (0.75), residues: 129 helix: 3.46 (1.31), residues: 12 sheet: 0.78 (0.60), residues: 79 loop : -1.65 (0.90), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 194 TYR 0.007 0.001 TYR A 235 PHE 0.009 0.001 PHE A 202 TRP 0.006 0.001 TRP A 179 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 1162) covalent geometry : angle 0.75234 ( 1589) SS BOND : bond 0.00278 ( 1) SS BOND : angle 0.77606 ( 2) hydrogen bonds : bond 0.03740 ( 54) hydrogen bonds : angle 4.76284 ( 141) link_BETA1-4 : bond 0.00076 ( 1) link_BETA1-4 : angle 2.14123 ( 3) link_NAG-ASN : bond 0.00820 ( 3) link_NAG-ASN : angle 3.78953 ( 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 14 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.024 Fit side-chains REVERT: A 36 ILE cc_start: 0.9034 (mm) cc_final: 0.8798 (mt) outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.0393 time to fit residues: 0.6548 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 : 0.040 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 0.0570 chunk 1 optimal weight: 0.2980 chunk 13 optimal weight: 0.0970 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.169170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.148016 restraints weight = 1768.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.150173 restraints weight = 1261.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.151983 restraints weight = 997.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.152680 restraints weight = 840.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.153564 restraints weight = 759.076| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 1167 Z= 0.184 Angle : 0.939 17.701 1603 Z= 0.429 Chirality : 0.065 0.530 178 Planarity : 0.007 0.067 193 Dihedral : 8.950 41.022 235 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.47 % Allowed : 16.05 % 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: 0.18 (0.74), residues: 129 helix: 3.51 (1.38), residues: 12 sheet: 0.73 (0.63), residues: 74 loop : -2.05 (0.74), residues: 43 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 0.009 0.001 PHE A 202 TRP 0.007 0.001 TRP A 179 HIS 0.001 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 1162) covalent geometry : angle 0.79739 ( 1589) SS BOND : bond 0.00291 ( 1) SS BOND : angle 0.74902 ( 2) hydrogen bonds : bond 0.03665 ( 54) hydrogen bonds : angle 4.78189 ( 141) link_BETA1-4 : bond 0.00006 ( 1) link_BETA1-4 : angle 2.28351 ( 3) link_NAG-ASN : bond 0.00368 ( 3) link_NAG-ASN : angle 6.55760 ( 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 15 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.039 Fit side-chains REVERT: A 36 ILE cc_start: 0.9069 (mm) cc_final: 0.8802 (mt) REVERT: A 80 MET cc_start: 0.7702 (mmm) cc_final: 0.7295 (mmm) outliers start: 2 outliers final: 1 residues processed: 14 average time/residue: 0.0224 time to fit residues: 0.4421 Evaluate side-chains 12 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.041 ------------------------------------------------------------------------------- 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: 0.0980 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 chunk 6 optimal weight: 0.0770 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.0970 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.0770 chunk 8 optimal weight: 0.1980 chunk 12 optimal weight: 0.1980 chunk 9 optimal weight: 0.0980 overall best weight: 0.0894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.173472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.151672 restraints weight = 1732.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.154290 restraints weight = 1181.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.156001 restraints weight = 910.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.157535 restraints weight = 756.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.158031 restraints weight = 659.013| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1167 Z= 0.117 Angle : 0.764 10.030 1603 Z= 0.363 Chirality : 0.070 0.635 178 Planarity : 0.006 0.051 193 Dihedral : 7.769 48.520 235 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.23 % Allowed : 14.81 % Favored : 83.95 % 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: 0.32 (0.74), residues: 129 helix: 4.43 (1.32), residues: 12 sheet: 0.74 (0.63), residues: 74 loop : -2.05 (0.71), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 237 TYR 0.007 0.001 TYR A 43 PHE 0.008 0.001 PHE A 39 TRP 0.007 0.001 TRP A 65 HIS 0.001 0.000 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 1162) covalent geometry : angle 0.67485 ( 1589) SS BOND : bond 0.00130 ( 1) SS BOND : angle 0.61967 ( 2) hydrogen bonds : bond 0.02989 ( 54) hydrogen bonds : angle 4.46700 ( 141) link_BETA1-4 : bond 0.00383 ( 1) link_BETA1-4 : angle 2.24301 ( 3) link_NAG-ASN : bond 0.00954 ( 3) link_NAG-ASN : angle 4.67210 ( 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 17 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.043 Fit side-chains REVERT: A 36 ILE cc_start: 0.8961 (mm) cc_final: 0.8656 (mt) REVERT: A 80 MET cc_start: 0.7635 (mmm) cc_final: 0.7371 (tpp) outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.0268 time to fit residues: 0.6012 Evaluate side-chains 14 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.042 ------------------------------------------------------------------------------- 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: 0.0970 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 11 optimal weight: 0.0050 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 chunk 2 optimal weight: 0.0770 chunk 0 optimal weight: 0.0770 chunk 6 optimal weight: 0.8980 overall best weight: 0.0666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.171579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.150152 restraints weight = 1706.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.152393 restraints weight = 1172.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.154555 restraints weight = 908.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.155849 restraints weight = 742.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.156777 restraints weight = 644.029| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1167 Z= 0.097 Angle : 0.628 6.821 1603 Z= 0.306 Chirality : 0.061 0.509 178 Planarity : 0.006 0.062 193 Dihedral : 6.488 33.647 235 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.47 % Allowed : 16.05 % 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: 0.37 (0.75), residues: 129 helix: 4.93 (1.28), residues: 12 sheet: 0.73 (0.64), residues: 74 loop : -2.11 (0.69), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 194 TYR 0.004 0.001 TYR A 43 PHE 0.015 0.001 PHE A 197 TRP 0.007 0.001 TRP A 65 HIS 0.000 0.000 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 1162) covalent geometry : angle 0.58384 ( 1589) SS BOND : bond 0.00128 ( 1) SS BOND : angle 0.57958 ( 2) hydrogen bonds : bond 0.02733 ( 54) hydrogen bonds : angle 4.38188 ( 141) link_BETA1-4 : bond 0.00211 ( 1) link_BETA1-4 : angle 2.10275 ( 3) link_NAG-ASN : bond 0.00230 ( 3) link_NAG-ASN : angle 2.90339 ( 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 16 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.038 Fit side-chains REVERT: A 36 ILE cc_start: 0.8836 (mm) cc_final: 0.8574 (mt) outliers start: 2 outliers final: 1 residues processed: 15 average time/residue: 0.0201 time to fit residues: 0.4002 Evaluate side-chains 14 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.051 ------------------------------------------------------------------------------- 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: 0.7980 chunk 3 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 2 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 chunk 4 optimal weight: 0.1980 chunk 9 optimal weight: 0.0670 chunk 8 optimal weight: 0.3980 chunk 11 optimal weight: 0.0970 overall best weight: 0.1052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.172065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.149938 restraints weight = 1774.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.152778 restraints weight = 1182.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.154601 restraints weight = 894.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155651 restraints weight = 743.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.156836 restraints weight = 657.841| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1167 Z= 0.103 Angle : 0.622 10.001 1603 Z= 0.307 Chirality : 0.055 0.348 178 Planarity : 0.006 0.052 193 Dihedral : 5.466 30.082 235 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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 : 0.77 % 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: 0.50 (0.75), residues: 129 helix: 5.06 (1.24), residues: 12 sheet: 0.82 (0.64), residues: 74 loop : -2.05 (0.72), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 194 TYR 0.005 0.001 TYR A 87 PHE 0.004 0.001 PHE A 202 TRP 0.007 0.001 TRP A 65 HIS 0.000 0.000 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 1162) covalent geometry : angle 0.53514 ( 1589) SS BOND : bond 0.00166 ( 1) SS BOND : angle 0.59716 ( 2) hydrogen bonds : bond 0.02780 ( 54) hydrogen bonds : angle 4.39047 ( 141) link_BETA1-4 : bond 0.00119 ( 1) link_BETA1-4 : angle 2.07865 ( 3) link_NAG-ASN : bond 0.00432 ( 3) link_NAG-ASN : angle 4.09085 ( 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 17 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.042 Fit side-chains REVERT: A 36 ILE cc_start: 0.8910 (mm) cc_final: 0.8639 (mt) REVERT: A 39 PHE cc_start: 0.9156 (t80) cc_final: 0.8697 (t80) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.0438 time to fit residues: 0.8787 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 : 0.043 ------------------------------------------------------------------------------- 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: 0.0170 chunk 1 optimal weight: 0.0980 chunk 9 optimal weight: 0.0970 chunk 4 optimal weight: 0.2980 chunk 12 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 0.0670 chunk 3 optimal weight: 0.0570 chunk 11 optimal weight: 0.0870 chunk 8 optimal weight: 0.0970 chunk 10 optimal weight: 0.6980 overall best weight: 0.0650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.171949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.150433 restraints weight = 1784.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.153066 restraints weight = 1232.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.154782 restraints weight = 955.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.156041 restraints weight = 799.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.156871 restraints weight = 702.866| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 1167 Z= 0.351 Angle : 1.950 59.198 1603 Z= 1.220 Chirality : 0.083 0.665 178 Planarity : 0.008 0.076 193 Dihedral : 5.384 29.708 235 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.23 % Allowed : 16.05 % Favored : 82.72 % 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: 0.48 (0.75), residues: 129 helix: 5.10 (1.23), residues: 12 sheet: 0.80 (0.64), residues: 74 loop : -2.08 (0.71), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 194 TYR 0.004 0.001 TYR A 43 PHE 0.003 0.001 PHE A 202 TRP 0.006 0.001 TRP A 65 HIS 0.000 0.000 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 1162) covalent geometry : angle 1.93320 ( 1589) SS BOND : bond 0.00152 ( 1) SS BOND : angle 0.55774 ( 2) hydrogen bonds : bond 0.02778 ( 54) hydrogen bonds : angle 4.39184 ( 141) link_BETA1-4 : bond 0.00872 ( 1) link_BETA1-4 : angle 2.06521 ( 3) link_NAG-ASN : bond 0.01081 ( 3) link_NAG-ASN : angle 3.96513 ( 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 17 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.042 Fit side-chains revert: symmetry clash REVERT: A 36 ILE cc_start: 0.8911 (mm) cc_final: 0.8641 (mt) REVERT: A 39 PHE cc_start: 0.9146 (t80) cc_final: 0.8701 (t80) outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.0457 time to fit residues: 0.9136 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 : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.0470 chunk 13 optimal weight: 8.9990 chunk 1 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 0.4980 chunk 11 optimal weight: 0.0970 chunk 9 optimal weight: 0.0870 chunk 4 optimal weight: 0.2980 overall best weight: 0.1254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** 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 = 0.3972 r_free = 0.3972 target = 0.173107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.152623 restraints weight = 1772.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.154901 restraints weight = 1276.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.156366 restraints weight = 1015.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.157634 restraints weight = 863.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.158094 restraints weight = 767.056| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 1167 Z= 0.351 Angle : 1.950 59.198 1603 Z= 1.220 Chirality : 0.083 0.665 178 Planarity : 0.008 0.076 193 Dihedral : 5.384 29.708 235 Min Nonbonded Distance : 1.341 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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 : 0.00 % 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: 0.48 (0.75), residues: 129 helix: 5.10 (1.23), residues: 12 sheet: 0.80 (0.64), residues: 74 loop : -2.08 (0.71), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 194 TYR 0.004 0.001 TYR A 43 PHE 0.003 0.001 PHE A 202 TRP 0.006 0.001 TRP A 65 HIS 0.000 0.000 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 1162) covalent geometry : angle 1.93320 ( 1589) SS BOND : bond 0.00152 ( 1) SS BOND : angle 0.55774 ( 2) hydrogen bonds : bond 0.02778 ( 54) hydrogen bonds : angle 4.39184 ( 141) link_BETA1-4 : bond 0.00872 ( 1) link_BETA1-4 : angle 2.06521 ( 3) link_NAG-ASN : bond 0.01081 ( 3) link_NAG-ASN : angle 3.96513 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 663.27 seconds wall clock time: 11 minutes 56.40 seconds (716.40 seconds total)