Starting phenix.real_space_refine on Wed Jul 23 07:03:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7usb_26731/07_2025/7usb_26731.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usb_26731/07_2025/7usb_26731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7usb_26731/07_2025/7usb_26731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usb_26731/07_2025/7usb_26731.map" model { file = "/net/cci-nas-00/data/ceres_data/7usb_26731/07_2025/7usb_26731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usb_26731/07_2025/7usb_26731.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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 12 5.16 5 C 1078 2.51 5 N 279 2.21 5 O 292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 1661 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain breaks: 5 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.12, per 1000 atoms: 2.48 Number of scatterers: 1661 At special positions: 0 Unit cell: (57.324, 67.44, 57.324, 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 12 16.00 O 292 8.00 N 279 7.00 C 1078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 68 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 170 " distance=2.04 Simple disulfide: pdb=" SG CYS A 250 " - pdb=" SG CYS A 254 " distance=2.13 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 A5401 " - " ASN A 242 " " NAG A5402 " - " ASN A 26 " " NAG A5403 " - " ASN A 42 " " NAG B 1 " - " ASN A 249 " Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 200.2 milliseconds 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 404 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 4 sheets defined 13.6% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 29 through 32 Processing helix chain 'A' and resid 33 through 44 Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 254 through 258 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 57 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 80 removed outlier: 7.297A pdb=" N PHE A 202 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LYS A 110 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR A 204 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 130 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU A 155 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE A 132 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS A 153 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 196 64 hydrogen bonds defined for protein. 150 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: 0.45 Time building geometry restraints manager: 0.56 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: 390 1.33 - 1.46: 470 1.46 - 1.58: 830 1.58 - 1.71: 1 1.71 - 1.84: 14 Bond restraints: 1705 Sorted by residual: bond pdb=" CB LEU A 207 " pdb=" CG LEU A 207 " ideal model delta sigma weight residual 1.530 1.602 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" CA PRO A 48 " pdb=" C PRO A 48 " ideal model delta sigma weight residual 1.514 1.534 -0.019 5.50e-03 3.31e+04 1.23e+01 bond pdb=" C5 NAG A5401 " pdb=" O5 NAG A5401 " ideal model delta sigma weight residual 1.413 1.478 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C5 NAG A5402 " pdb=" O5 NAG A5402 " ideal model delta sigma weight residual 1.413 1.475 -0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" NE ARG A 194 " pdb=" CZ ARG A 194 " ideal model delta sigma weight residual 1.326 1.358 -0.032 1.10e-02 8.26e+03 8.45e+00 ... (remaining 1700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.50: 2285 4.50 - 8.99: 46 8.99 - 13.49: 2 13.49 - 17.98: 2 17.98 - 22.48: 2 Bond angle restraints: 2337 Sorted by residual: angle pdb=" CD1 LEU A 41 " pdb=" CG LEU A 41 " pdb=" CD2 LEU A 41 " ideal model delta sigma weight residual 110.80 133.28 -22.48 2.20e+00 2.07e-01 1.04e+02 angle pdb=" C LEU A 47 " pdb=" N PRO A 48 " pdb=" CA PRO A 48 " ideal model delta sigma weight residual 119.66 127.07 -7.41 7.30e-01 1.88e+00 1.03e+02 angle pdb=" CG1 VAL A 185 " pdb=" CB VAL A 185 " pdb=" CG2 VAL A 185 " ideal model delta sigma weight residual 110.80 131.09 -20.29 2.20e+00 2.07e-01 8.50e+01 angle pdb=" C PRO A 48 " pdb=" N PRO A 49 " pdb=" CA PRO A 49 " ideal model delta sigma weight residual 119.56 127.28 -7.72 1.01e+00 9.80e-01 5.84e+01 angle pdb=" C PRO A 137 " pdb=" N PRO A 138 " pdb=" CA PRO A 138 " ideal model delta sigma weight residual 120.03 126.02 -5.99 9.90e-01 1.02e+00 3.67e+01 ... (remaining 2332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 992 17.81 - 35.63: 39 35.63 - 53.44: 7 53.44 - 71.25: 6 71.25 - 89.07: 1 Dihedral angle restraints: 1045 sinusoidal: 422 harmonic: 623 Sorted by residual: dihedral pdb=" CB CYS A 21 " pdb=" SG CYS A 21 " pdb=" SG CYS A 68 " pdb=" CB CYS A 68 " ideal model delta sinusoidal sigma weight residual 93.00 162.97 -69.97 1 1.00e+01 1.00e-02 6.31e+01 dihedral pdb=" CB CYS A 250 " pdb=" SG CYS A 250 " pdb=" SG CYS A 254 " pdb=" CB CYS A 254 " ideal model delta sinusoidal sigma weight residual 93.00 153.68 -60.68 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual -86.00 -142.30 56.30 1 1.00e+01 1.00e-02 4.27e+01 ... (remaining 1042 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.109: 226 0.109 - 0.216: 31 0.216 - 0.323: 11 0.323 - 0.430: 6 0.430 - 0.537: 2 Chirality restraints: 276 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 -2.50 0.10 2.00e-02 2.50e+03 2.73e+01 chirality pdb=" CG LEU A 41 " pdb=" CB LEU A 41 " pdb=" CD1 LEU A 41 " pdb=" CD2 LEU A 41 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.21e+00 chirality pdb=" CB VAL A 185 " pdb=" CA VAL A 185 " pdb=" CG1 VAL A 185 " pdb=" CG2 VAL A 185 " both_signs ideal model delta sigma weight residual False -2.63 -2.10 -0.52 2.00e-01 2.50e+01 6.87e+00 ... (remaining 273 not shown) Planarity restraints: 293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A5403 " -0.211 2.00e-02 2.50e+03 1.79e-01 4.01e+02 pdb=" C7 NAG A5403 " 0.043 2.00e-02 2.50e+03 pdb=" C8 NAG A5403 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG A5403 " 0.294 2.00e-02 2.50e+03 pdb=" O7 NAG A5403 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.103 2.00e-02 2.50e+03 8.70e-02 9.46e+01 pdb=" C7 NAG B 2 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.028 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.138 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 133 " -0.021 2.00e-02 2.50e+03 4.13e-02 1.70e+01 pdb=" C CYS A 133 " 0.071 2.00e-02 2.50e+03 pdb=" O CYS A 133 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS A 134 " -0.024 2.00e-02 2.50e+03 ... (remaining 290 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 931 3.05 - 3.51: 1400 3.51 - 3.98: 2544 3.98 - 4.44: 2901 4.44 - 4.90: 4618 Nonbonded interactions: 12394 Sorted by model distance: nonbonded pdb=" N GLY A 243 " pdb=" N THR A 244 " model vdw 2.590 2.560 nonbonded pdb=" N PHE A 202 " pdb=" O PHE A 202 " model vdw 2.614 2.496 nonbonded pdb=" O LYS A 110 " pdb=" CD PRO A 111 " model vdw 2.626 2.752 nonbonded pdb=" OD1 ASP A 89 " pdb=" N TYR A 90 " model vdw 2.634 3.120 nonbonded pdb=" N GLN A 167 " pdb=" O GLN A 167 " model vdw 2.647 2.496 ... (remaining 12389 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.540 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 12.370 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 : 0.013 0.100 1715 Z= 0.730 Angle : 1.738 22.477 2362 Z= 1.051 Chirality : 0.110 0.537 276 Planarity : 0.013 0.179 289 Dihedral : 10.319 89.066 626 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.39 % Allowed : 1.39 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.53), residues: 201 helix: -1.80 (0.97), residues: 18 sheet: 1.28 (0.53), residues: 75 loop : -1.01 (0.52), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP A 88 HIS 0.003 0.001 HIS A 189 PHE 0.009 0.003 PHE A 227 TYR 0.023 0.005 TYR A 90 ARG 0.001 0.000 ARG A 46 Details of bonding type rmsd link_NAG-ASN : bond 0.05775 ( 4) link_NAG-ASN : angle 2.53008 ( 12) link_BETA1-4 : bond 0.00680 ( 1) link_BETA1-4 : angle 4.32483 ( 3) hydrogen bonds : bond 0.17079 ( 64) hydrogen bonds : angle 6.90121 ( 150) SS BOND : bond 0.04489 ( 5) SS BOND : angle 2.96757 ( 10) covalent geometry : bond 0.01297 ( 1705) covalent geometry : angle 1.72012 ( 2337) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.170 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.1073 time to fit residues: 4.5283 Evaluate side-chains 18 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 0.3980 chunk 15 optimal weight: 0.0980 chunk 8 optimal weight: 0.1980 chunk 5 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 6 optimal weight: 0.0770 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 20 optimal weight: 0.4980 chunk 18 optimal weight: 0.1980 overall best weight: 0.1338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.180870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.152993 restraints weight = 2012.404| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.41 r_work: 0.3637 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1715 Z= 0.145 Angle : 0.677 5.891 2362 Z= 0.360 Chirality : 0.049 0.241 276 Planarity : 0.004 0.032 289 Dihedral : 5.452 23.045 331 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.39 % Allowed : 5.56 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.54), residues: 201 helix: 1.72 (1.41), residues: 12 sheet: 1.02 (0.56), residues: 75 loop : -1.15 (0.50), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 88 HIS 0.002 0.001 HIS A 189 PHE 0.011 0.001 PHE A 24 TYR 0.008 0.001 TYR A 175 ARG 0.002 0.000 ARG A 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 4) link_NAG-ASN : angle 3.20241 ( 12) link_BETA1-4 : bond 0.00233 ( 1) link_BETA1-4 : angle 2.65741 ( 3) hydrogen bonds : bond 0.05323 ( 64) hydrogen bonds : angle 5.32767 ( 150) SS BOND : bond 0.00275 ( 5) SS BOND : angle 0.63954 ( 10) covalent geometry : bond 0.00319 ( 1705) covalent geometry : angle 0.63183 ( 2337) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.193 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 21 average time/residue: 0.1837 time to fit residues: 4.5194 Evaluate side-chains 18 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 2 optimal weight: 0.0270 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 overall best weight: 0.2438 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.192259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.163024 restraints weight = 1927.341| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.43 r_work: 0.3596 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1715 Z= 0.157 Angle : 0.642 6.557 2362 Z= 0.330 Chirality : 0.049 0.247 276 Planarity : 0.004 0.035 289 Dihedral : 5.267 23.984 330 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.39 % Allowed : 6.25 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.54), residues: 201 helix: 1.20 (1.34), residues: 13 sheet: 0.54 (0.57), residues: 75 loop : -1.52 (0.51), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 88 HIS 0.001 0.000 HIS A 189 PHE 0.012 0.002 PHE A 180 TYR 0.009 0.001 TYR A 112 ARG 0.002 0.000 ARG A 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 4) link_NAG-ASN : angle 3.19295 ( 12) link_BETA1-4 : bond 0.00007 ( 1) link_BETA1-4 : angle 2.24808 ( 3) hydrogen bonds : bond 0.04173 ( 64) hydrogen bonds : angle 5.01044 ( 150) SS BOND : bond 0.00499 ( 5) SS BOND : angle 0.80341 ( 10) covalent geometry : bond 0.00369 ( 1705) covalent geometry : angle 0.59580 ( 2337) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.170 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 0.1314 time to fit residues: 3.3163 Evaluate side-chains 19 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 0.1980 chunk 16 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.170931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140343 restraints weight = 1948.876| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.48 r_work: 0.3513 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 1715 Z= 0.208 Angle : 0.674 6.762 2362 Z= 0.340 Chirality : 0.052 0.273 276 Planarity : 0.004 0.033 289 Dihedral : 5.771 24.921 330 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.08 % Allowed : 8.33 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.57), residues: 201 helix: 0.81 (1.30), residues: 13 sheet: 0.33 (0.60), residues: 73 loop : -1.65 (0.54), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 88 HIS 0.004 0.001 HIS A 189 PHE 0.024 0.002 PHE A 159 TYR 0.008 0.001 TYR A 58 ARG 0.002 0.000 ARG A 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 4) link_NAG-ASN : angle 3.58801 ( 12) link_BETA1-4 : bond 0.00352 ( 1) link_BETA1-4 : angle 2.45332 ( 3) hydrogen bonds : bond 0.04137 ( 64) hydrogen bonds : angle 5.07679 ( 150) SS BOND : bond 0.00369 ( 5) SS BOND : angle 0.54470 ( 10) covalent geometry : bond 0.00501 ( 1705) covalent geometry : angle 0.61976 ( 2337) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.189 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.1328 time to fit residues: 3.5450 Evaluate side-chains 22 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.0170 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 3 optimal weight: 0.0980 chunk 9 optimal weight: 0.0870 chunk 17 optimal weight: 0.4980 chunk 18 optimal weight: 0.0870 chunk 14 optimal weight: 0.1980 chunk 1 optimal weight: 0.0980 overall best weight: 0.0774 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.174526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.144176 restraints weight = 1939.050| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.47 r_work: 0.3771 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 1715 Z= 0.097 Angle : 0.537 5.536 2362 Z= 0.277 Chirality : 0.046 0.237 276 Planarity : 0.003 0.030 289 Dihedral : 5.199 24.931 330 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.08 % Allowed : 10.42 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.58), residues: 201 helix: 1.04 (1.32), residues: 13 sheet: 0.36 (0.61), residues: 74 loop : -1.46 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 88 HIS 0.001 0.000 HIS A 104 PHE 0.019 0.001 PHE A 159 TYR 0.005 0.001 TYR A 112 ARG 0.001 0.000 ARG A 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 4) link_NAG-ASN : angle 2.72324 ( 12) link_BETA1-4 : bond 0.00153 ( 1) link_BETA1-4 : angle 1.84078 ( 3) hydrogen bonds : bond 0.03419 ( 64) hydrogen bonds : angle 4.78465 ( 150) SS BOND : bond 0.00126 ( 5) SS BOND : angle 0.57758 ( 10) covalent geometry : bond 0.00217 ( 1705) covalent geometry : angle 0.49709 ( 2337) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.172 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 21 average time/residue: 0.1230 time to fit residues: 3.1465 Evaluate side-chains 25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.0970 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 10 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 0.1980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.178353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148208 restraints weight = 1996.657| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.49 r_work: 0.3526 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1715 Z= 0.149 Angle : 0.596 5.649 2362 Z= 0.300 Chirality : 0.048 0.247 276 Planarity : 0.003 0.029 289 Dihedral : 5.288 25.444 330 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.08 % Allowed : 11.81 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.58), residues: 201 helix: 1.04 (1.32), residues: 13 sheet: 0.27 (0.61), residues: 73 loop : -1.56 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 88 HIS 0.001 0.000 HIS A 32 PHE 0.006 0.001 PHE A 159 TYR 0.005 0.001 TYR A 58 ARG 0.001 0.000 ARG A 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 4) link_NAG-ASN : angle 3.02315 ( 12) link_BETA1-4 : bond 0.00109 ( 1) link_BETA1-4 : angle 2.09692 ( 3) hydrogen bonds : bond 0.03643 ( 64) hydrogen bonds : angle 4.82078 ( 150) SS BOND : bond 0.00198 ( 5) SS BOND : angle 0.45006 ( 10) covalent geometry : bond 0.00356 ( 1705) covalent geometry : angle 0.55241 ( 2337) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 173 MET cc_start: 0.7611 (pmm) cc_final: 0.6852 (ptt) outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.1328 time to fit residues: 3.6752 Evaluate side-chains 24 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.0040 chunk 14 optimal weight: 0.0970 chunk 8 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.0980 overall best weight: 0.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.178896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148981 restraints weight = 1974.607| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.47 r_work: 0.3533 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1715 Z= 0.129 Angle : 0.568 5.450 2362 Z= 0.287 Chirality : 0.047 0.241 276 Planarity : 0.003 0.029 289 Dihedral : 5.243 25.020 330 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.08 % Allowed : 12.50 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.58), residues: 201 helix: 1.08 (1.32), residues: 13 sheet: 0.13 (0.61), residues: 74 loop : -1.52 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 88 HIS 0.001 0.000 HIS A 32 PHE 0.003 0.001 PHE A 180 TYR 0.004 0.001 TYR A 112 ARG 0.001 0.000 ARG A 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 4) link_NAG-ASN : angle 2.85709 ( 12) link_BETA1-4 : bond 0.00042 ( 1) link_BETA1-4 : angle 1.98235 ( 3) hydrogen bonds : bond 0.03547 ( 64) hydrogen bonds : angle 4.76907 ( 150) SS BOND : bond 0.00166 ( 5) SS BOND : angle 0.45064 ( 10) covalent geometry : bond 0.00305 ( 1705) covalent geometry : angle 0.52731 ( 2337) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 173 MET cc_start: 0.7598 (pmm) cc_final: 0.6974 (ptt) outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.1286 time to fit residues: 3.5437 Evaluate side-chains 25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.0060 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 6 optimal weight: 0.0870 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.174734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144753 restraints weight = 1967.976| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.45 r_work: 0.3503 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1715 Z= 0.183 Angle : 0.635 6.139 2362 Z= 0.315 Chirality : 0.050 0.256 276 Planarity : 0.004 0.030 289 Dihedral : 5.676 25.939 330 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.08 % Allowed : 11.81 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.58), residues: 201 helix: 0.95 (1.33), residues: 13 sheet: -0.01 (0.61), residues: 73 loop : -1.58 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 88 HIS 0.001 0.001 HIS A 32 PHE 0.005 0.001 PHE A 197 TYR 0.004 0.001 TYR A 58 ARG 0.001 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 4) link_NAG-ASN : angle 3.33141 ( 12) link_BETA1-4 : bond 0.00299 ( 1) link_BETA1-4 : angle 2.29063 ( 3) hydrogen bonds : bond 0.03829 ( 64) hydrogen bonds : angle 4.96808 ( 150) SS BOND : bond 0.00249 ( 5) SS BOND : angle 0.47862 ( 10) covalent geometry : bond 0.00438 ( 1705) covalent geometry : angle 0.58551 ( 2337) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 173 MET cc_start: 0.7686 (pmm) cc_final: 0.7179 (ptt) outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.1507 time to fit residues: 4.4103 Evaluate side-chains 26 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 4 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.0060 chunk 16 optimal weight: 0.1980 chunk 5 optimal weight: 0.2980 chunk 11 optimal weight: 0.0050 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.1980 overall best weight: 0.0988 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.173554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.143575 restraints weight = 1985.083| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.50 r_work: 0.3739 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 1715 Z= 0.142 Angle : 0.749 14.428 2362 Z= 0.374 Chirality : 0.047 0.235 276 Planarity : 0.003 0.029 289 Dihedral : 5.539 24.987 330 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.78 % Allowed : 11.11 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.57), residues: 201 helix: 1.16 (1.33), residues: 13 sheet: -0.12 (0.62), residues: 74 loop : -1.75 (0.54), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 88 HIS 0.001 0.000 HIS A 32 PHE 0.002 0.001 PHE A 180 TYR 0.005 0.001 TYR A 43 ARG 0.000 0.000 ARG A 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00950 ( 4) link_NAG-ASN : angle 3.15906 ( 12) link_BETA1-4 : bond 0.00026 ( 1) link_BETA1-4 : angle 1.70779 ( 3) hydrogen bonds : bond 0.03413 ( 64) hydrogen bonds : angle 4.79141 ( 150) SS BOND : bond 0.00162 ( 5) SS BOND : angle 4.77505 ( 10) covalent geometry : bond 0.00343 ( 1705) covalent geometry : angle 0.64432 ( 2337) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 173 MET cc_start: 0.7467 (pmm) cc_final: 0.7234 (ptt) outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 0.1429 time to fit residues: 4.5279 Evaluate side-chains 27 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 18 optimal weight: 0.0770 chunk 1 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.169765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.138848 restraints weight = 2039.251| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.60 r_work: 0.3469 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 1715 Z= 0.193 Angle : 0.761 12.669 2362 Z= 0.378 Chirality : 0.049 0.251 276 Planarity : 0.004 0.029 289 Dihedral : 5.932 27.025 330 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.08 % Allowed : 13.19 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.57), residues: 201 helix: 1.05 (1.34), residues: 13 sheet: -0.01 (0.61), residues: 72 loop : -1.82 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 179 HIS 0.001 0.000 HIS A 32 PHE 0.004 0.001 PHE A 180 TYR 0.006 0.001 TYR A 77 ARG 0.001 0.000 ARG A 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00825 ( 4) link_NAG-ASN : angle 3.35100 ( 12) link_BETA1-4 : bond 0.00287 ( 1) link_BETA1-4 : angle 1.80535 ( 3) hydrogen bonds : bond 0.04074 ( 64) hydrogen bonds : angle 4.97604 ( 150) SS BOND : bond 0.00171 ( 5) SS BOND : angle 3.89685 ( 10) covalent geometry : bond 0.00478 ( 1705) covalent geometry : angle 0.67709 ( 2337) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 173 MET cc_start: 0.7776 (pmm) cc_final: 0.7307 (ptt) outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.1456 time to fit residues: 4.4322 Evaluate side-chains 26 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 13 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 3 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 overall best weight: 0.2378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.170286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139518 restraints weight = 2023.785| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.63 r_work: 0.3479 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 1715 Z= 0.172 Angle : 0.702 9.686 2362 Z= 0.354 Chirality : 0.049 0.247 276 Planarity : 0.003 0.029 289 Dihedral : 5.895 26.777 330 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.08 % Allowed : 13.89 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.57), residues: 201 helix: 1.06 (1.33), residues: 13 sheet: -0.25 (0.61), residues: 74 loop : -1.77 (0.54), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 88 HIS 0.001 0.000 HIS A 32 PHE 0.003 0.001 PHE A 180 TYR 0.006 0.001 TYR A 77 ARG 0.001 0.000 ARG A 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 4) link_NAG-ASN : angle 3.32532 ( 12) link_BETA1-4 : bond 0.00294 ( 1) link_BETA1-4 : angle 1.84236 ( 3) hydrogen bonds : bond 0.03896 ( 64) hydrogen bonds : angle 4.95718 ( 150) SS BOND : bond 0.00256 ( 5) SS BOND : angle 3.16702 ( 10) covalent geometry : bond 0.00430 ( 1705) covalent geometry : angle 0.62776 ( 2337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1817.60 seconds wall clock time: 32 minutes 10.45 seconds (1930.45 seconds total)