Starting phenix.real_space_refine on Wed Jul 1 23:36:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwn_47258/07_2026/9dwn_47258.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwn_47258/07_2026/9dwn_47258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dwn_47258/07_2026/9dwn_47258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwn_47258/07_2026/9dwn_47258.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwn_47258/07_2026/9dwn_47258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwn_47258/07_2026/9dwn_47258.cif" } resolution = 3.2 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 5 8.98 5 S 28 5.16 5 C 2819 2.51 5 N 709 2.21 5 O 764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4325 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2133 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2129 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' K': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Ad-hoc single atom residues: {' K': 3} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 3 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.18, per 1000 atoms: 0.27 Number of scatterers: 4325 At special positions: 0 Unit cell: (73.4033, 66.2225, 102.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 5 19.00 S 28 16.00 O 764 8.00 N 709 7.00 C 2819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 NAG-ASN " NAG A 401 " - " ASN A 59 " " NAG A 402 " - " ASN A 65 " " NAG B 401 " - " ASN B 59 " " NAG B 402 " - " ASN B 65 " Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 110.6 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 996 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 82.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 14 through 65 removed outlier: 5.539A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N HIS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 120 through 170 removed outlier: 4.275A pdb=" N SER A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 221 Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 253 through 297 removed outlier: 3.538A pdb=" N GLY A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 65 removed outlier: 5.282A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 85 removed outlier: 3.549A pdb=" N ALA B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 120 through 170 removed outlier: 4.034A pdb=" N VAL B 133 " --> pdb=" O PHE B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 221 Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 223 through 236 Processing helix chain 'B' and resid 253 through 297 376 hydrogen bonds defined for protein. 1128 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: 0.56 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1331 1.34 - 1.46: 818 1.46 - 1.57: 2233 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 4422 Sorted by residual: bond pdb=" C1 NAG A 401 " pdb=" O5 NAG A 401 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 NAG B 402 " pdb=" O5 NAG B 402 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.86e+00 bond pdb=" C1 NAG B 401 " pdb=" O5 NAG B 401 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" CA LEU B 187 " pdb=" C LEU B 187 " ideal model delta sigma weight residual 1.529 1.515 0.014 9.30e-03 1.16e+04 2.39e+00 bond pdb=" C1 NAG A 402 " pdb=" O5 NAG A 402 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.37e+00 ... (remaining 4417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 5858 1.70 - 3.41: 113 3.41 - 5.11: 8 5.11 - 6.82: 8 6.82 - 8.52: 1 Bond angle restraints: 5988 Sorted by residual: angle pdb=" C LEU B 187 " pdb=" CA LEU B 187 " pdb=" CB LEU B 187 " ideal model delta sigma weight residual 116.54 109.90 6.64 1.15e+00 7.56e-01 3.33e+01 angle pdb=" N GLY B 189 " pdb=" CA GLY B 189 " pdb=" C GLY B 189 " ideal model delta sigma weight residual 112.64 106.87 5.77 1.21e+00 6.83e-01 2.27e+01 angle pdb=" CA LEU B 187 " pdb=" C LEU B 187 " pdb=" N ALA B 188 " ideal model delta sigma weight residual 119.52 116.68 2.84 7.90e-01 1.60e+00 1.29e+01 angle pdb=" N ILE A 111 " pdb=" CA ILE A 111 " pdb=" C ILE A 111 " ideal model delta sigma weight residual 111.45 108.15 3.30 9.30e-01 1.16e+00 1.26e+01 angle pdb=" N ILE B 111 " pdb=" CA ILE B 111 " pdb=" C ILE B 111 " ideal model delta sigma weight residual 110.74 107.87 2.87 9.10e-01 1.21e+00 9.92e+00 ... (remaining 5983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.48: 2415 22.48 - 44.97: 151 44.97 - 67.45: 11 67.45 - 89.94: 4 89.94 - 112.42: 3 Dihedral angle restraints: 2584 sinusoidal: 1026 harmonic: 1558 Sorted by residual: dihedral pdb=" CA ASP B 89 " pdb=" C ASP B 89 " pdb=" N ASN B 90 " pdb=" CA ASN B 90 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA TRP A 95 " pdb=" C TRP A 95 " pdb=" N ASP A 96 " pdb=" CA ASP A 96 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ASP A 89 " pdb=" C ASP A 89 " pdb=" N ASN A 90 " pdb=" CA ASN A 90 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 2581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 635 0.073 - 0.145: 43 0.145 - 0.218: 2 0.218 - 0.290: 0 0.290 - 0.363: 1 Chirality restraints: 681 Sorted by residual: chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 65 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 59 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 59 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 678 not shown) Planarity restraints: 743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 117 " -0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 118 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 118 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 118 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 102 " 0.005 2.00e-02 2.50e+03 7.56e-03 1.14e+00 pdb=" CG TYR A 102 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 102 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 102 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 102 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 102 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 102 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 102 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 131 " 0.005 2.00e-02 2.50e+03 1.07e-02 1.14e+00 pdb=" C GLY A 131 " -0.018 2.00e-02 2.50e+03 pdb=" O GLY A 131 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU A 132 " 0.006 2.00e-02 2.50e+03 ... (remaining 740 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.76: 781 2.76 - 3.36: 5215 3.36 - 3.95: 8720 3.95 - 4.54: 12104 4.54 - 5.14: 17276 Nonbonded interactions: 44096 Sorted by model distance: nonbonded pdb=" CD1 ILE A 139 " pdb=" O HOH A 501 " model vdw 2.165 3.460 nonbonded pdb=" CG1 ILE B 139 " pdb=" O HOH B 501 " model vdw 2.219 3.440 nonbonded pdb=" OH TYR A 273 " pdb=" OH TYR B 273 " model vdw 2.236 3.040 nonbonded pdb=" O GLY B 105 " pdb=" OG SER B 109 " model vdw 2.272 3.040 nonbonded pdb=" OH TYR B 216 " pdb=" OD1 ASN B 261 " model vdw 2.273 3.040 ... (remaining 44091 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 157 or (resid 158 and (name N or name CA or nam \ e C or name O or name CB )) or resid 159 through 170 or resid 186 through 404)) selection = (chain 'B' and resid 14 through 404) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.010 Process input model: 4.880 Find NCS groups from input model: 0.060 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.004 0.090 4426 Z= 0.180 Angle : 0.629 13.001 6000 Z= 0.338 Chirality : 0.039 0.363 681 Planarity : 0.003 0.031 739 Dihedral : 14.430 112.419 1588 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.45 % Allowed : 0.00 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.34), residues: 532 helix: 2.65 (0.21), residues: 423 sheet: None (None), residues: 0 loop : -2.30 (0.58), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 94 TYR 0.018 0.002 TYR A 102 PHE 0.015 0.001 PHE A 126 TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 ( 4422) covalent geometry : angle 0.59431 / 0.33 ( 5988) hydrogen bonds : bond 0.10020 / 6.53 ( 376) hydrogen bonds : angle 4.89116 / 3.75 ( 1128) link_NAG-ASN : bond 0.01115 / 0.56 ( 4) link_NAG-ASN : angle 4.62833 / 2.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.141 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 32 average time/residue: 0.0341 time to fit residues: 1.7401 Evaluate side-chains 28 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.174673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.131048 restraints weight = 4036.560| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.89 r_work: 0.3158 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4426 Z= 0.160 Angle : 0.578 10.985 6000 Z= 0.296 Chirality : 0.039 0.309 681 Planarity : 0.003 0.021 739 Dihedral : 8.649 86.214 676 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.67 % Allowed : 4.27 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.56 (0.35), residues: 532 helix: 3.25 (0.22), residues: 425 sheet: None (None), residues: 0 loop : -1.70 (0.60), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.014 0.001 TYR B 257 PHE 0.015 0.001 PHE A 126 TRP 0.007 0.001 TRP B 190 HIS 0.001 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 4422) covalent geometry : angle 0.55170 / 0.29 ( 5988) hydrogen bonds : bond 0.04045 / 2.73 ( 376) hydrogen bonds : angle 3.84544 / 2.91 ( 1128) link_NAG-ASN : bond 0.00791 / 0.40 ( 4) link_NAG-ASN : angle 3.86597 / 2.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.133 Fit side-chains REVERT: A 115 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.5959 (ptp) outliers start: 3 outliers final: 1 residues processed: 31 average time/residue: 0.0321 time to fit residues: 1.6199 Evaluate side-chains 29 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 115 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.170958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.123766 restraints weight = 4012.364| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.73 r_work: 0.3096 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4426 Z= 0.177 Angle : 0.577 10.013 6000 Z= 0.297 Chirality : 0.038 0.304 681 Planarity : 0.003 0.017 739 Dihedral : 5.518 52.068 676 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.35 % Allowed : 5.62 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.66 (0.35), residues: 532 helix: 3.27 (0.22), residues: 428 sheet: None (None), residues: 0 loop : -1.60 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.012 0.001 TYR B 257 PHE 0.015 0.002 PHE A 126 TRP 0.004 0.001 TRP A 53 HIS 0.001 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 4422) covalent geometry : angle 0.54591 / 0.29 ( 5988) hydrogen bonds : bond 0.04125 / 2.80 ( 376) hydrogen bonds : angle 3.86021 / 2.92 ( 1128) link_NAG-ASN : bond 0.00819 / 0.41 ( 4) link_NAG-ASN : angle 4.23996 / 2.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.098 Fit side-chains REVERT: A 115 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6135 (ptp) outliers start: 6 outliers final: 5 residues processed: 33 average time/residue: 0.0283 time to fit residues: 1.5147 Evaluate side-chains 36 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 256 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.171607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129722 restraints weight = 3980.608| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.48 r_work: 0.3152 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4426 Z= 0.150 Angle : 0.523 8.957 6000 Z= 0.277 Chirality : 0.037 0.305 681 Planarity : 0.002 0.016 739 Dihedral : 5.233 51.832 676 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.80 % Allowed : 7.64 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.75 (0.35), residues: 532 helix: 3.36 (0.22), residues: 428 sheet: None (None), residues: 0 loop : -1.72 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.012 0.001 TYR B 257 PHE 0.014 0.001 PHE A 126 TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 4422) covalent geometry : angle 0.50122 / 0.27 ( 5988) hydrogen bonds : bond 0.03967 / 2.69 ( 376) hydrogen bonds : angle 3.77734 / 2.86 ( 1128) link_NAG-ASN : bond 0.00698 / 0.35 ( 4) link_NAG-ASN : angle 3.34225 / 1.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.135 Fit side-chains REVERT: A 115 MET cc_start: 0.6514 (OUTLIER) cc_final: 0.5950 (ptp) REVERT: A 248 ASN cc_start: 0.8002 (p0) cc_final: 0.7699 (p0) outliers start: 8 outliers final: 5 residues processed: 33 average time/residue: 0.0339 time to fit residues: 1.7845 Evaluate side-chains 35 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 256 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.170716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.128021 restraints weight = 3969.408| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.52 r_work: 0.3126 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4426 Z= 0.160 Angle : 0.524 8.267 6000 Z= 0.280 Chirality : 0.037 0.302 681 Planarity : 0.002 0.015 739 Dihedral : 5.184 51.588 676 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.25 % Allowed : 7.64 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.80 (0.35), residues: 532 helix: 3.39 (0.22), residues: 428 sheet: None (None), residues: 0 loop : -1.66 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.012 0.001 TYR B 257 PHE 0.014 0.001 PHE A 126 TRP 0.004 0.001 TRP A 53 HIS 0.001 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 4422) covalent geometry : angle 0.50663 / 0.28 ( 5988) hydrogen bonds : bond 0.03999 / 2.71 ( 376) hydrogen bonds : angle 3.79125 / 2.86 ( 1128) link_NAG-ASN : bond 0.00626 / 0.31 ( 4) link_NAG-ASN : angle 3.07047 / 1.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.159 Fit side-chains REVERT: A 115 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.6134 (ptp) outliers start: 10 outliers final: 7 residues processed: 33 average time/residue: 0.0406 time to fit residues: 2.1458 Evaluate side-chains 34 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 256 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.171394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.128684 restraints weight = 4055.511| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.56 r_work: 0.3144 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4426 Z= 0.159 Angle : 0.520 7.636 6000 Z= 0.278 Chirality : 0.037 0.294 681 Planarity : 0.002 0.015 739 Dihedral : 5.170 51.327 676 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.25 % Allowed : 7.87 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.83 (0.35), residues: 532 helix: 3.40 (0.22), residues: 428 sheet: None (None), residues: 0 loop : -1.60 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.012 0.001 TYR B 257 PHE 0.014 0.001 PHE A 126 TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 4422) covalent geometry : angle 0.50506 / 0.28 ( 5988) hydrogen bonds : bond 0.03993 / 2.71 ( 376) hydrogen bonds : angle 3.79115 / 2.86 ( 1128) link_NAG-ASN : bond 0.00578 / 0.29 ( 4) link_NAG-ASN : angle 2.80909 / 1.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.172 Fit side-chains REVERT: A 115 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.6263 (ptp) outliers start: 10 outliers final: 8 residues processed: 32 average time/residue: 0.0465 time to fit residues: 2.3769 Evaluate side-chains 35 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 256 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.171141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.128508 restraints weight = 4004.828| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.54 r_work: 0.3147 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4426 Z= 0.148 Angle : 0.510 7.478 6000 Z= 0.273 Chirality : 0.036 0.299 681 Planarity : 0.002 0.016 739 Dihedral : 5.135 51.564 676 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.02 % Allowed : 8.76 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.88 (0.35), residues: 532 helix: 3.45 (0.22), residues: 428 sheet: None (None), residues: 0 loop : -1.61 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 92 TYR 0.011 0.001 TYR B 257 PHE 0.014 0.001 PHE A 126 TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 4422) covalent geometry : angle 0.49596 / 0.27 ( 5988) hydrogen bonds : bond 0.03932 / 2.66 ( 376) hydrogen bonds : angle 3.76248 / 2.83 ( 1128) link_NAG-ASN : bond 0.00597 / 0.30 ( 4) link_NAG-ASN : angle 2.73302 / 1.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.090 Fit side-chains REVERT: A 115 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.6270 (ptp) outliers start: 9 outliers final: 8 residues processed: 30 average time/residue: 0.0413 time to fit residues: 1.9504 Evaluate side-chains 34 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 256 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 21 optimal weight: 0.0020 chunk 10 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.175928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.131994 restraints weight = 4000.804| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.81 r_work: 0.3172 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4426 Z= 0.130 Angle : 0.486 6.812 6000 Z= 0.261 Chirality : 0.036 0.275 681 Planarity : 0.002 0.016 739 Dihedral : 5.048 51.893 676 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.02 % Allowed : 8.76 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.04 (0.35), residues: 532 helix: 3.58 (0.22), residues: 426 sheet: None (None), residues: 0 loop : -1.55 (0.60), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 92 TYR 0.011 0.001 TYR A 78 PHE 0.014 0.001 PHE A 126 TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 4422) covalent geometry : angle 0.47401 / 0.26 ( 5988) hydrogen bonds : bond 0.03789 / 2.56 ( 376) hydrogen bonds : angle 3.66462 / 2.76 ( 1128) link_NAG-ASN : bond 0.00550 / 0.27 ( 4) link_NAG-ASN : angle 2.44102 / 1.38 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.145 Fit side-chains REVERT: A 115 MET cc_start: 0.6057 (OUTLIER) cc_final: 0.5800 (ptp) outliers start: 9 outliers final: 8 residues processed: 32 average time/residue: 0.0308 time to fit residues: 1.5962 Evaluate side-chains 34 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 256 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 41 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.176873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.131420 restraints weight = 4027.943| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.99 r_work: 0.3134 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4426 Z= 0.137 Angle : 0.492 6.744 6000 Z= 0.265 Chirality : 0.036 0.270 681 Planarity : 0.002 0.016 739 Dihedral : 5.056 51.787 676 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.25 % Allowed : 8.99 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.06 (0.35), residues: 532 helix: 3.56 (0.22), residues: 428 sheet: None (None), residues: 0 loop : -1.51 (0.62), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 92 TYR 0.011 0.001 TYR B 257 PHE 0.014 0.001 PHE A 126 TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 4422) covalent geometry : angle 0.48107 / 0.26 ( 5988) hydrogen bonds : bond 0.03830 / 2.59 ( 376) hydrogen bonds : angle 3.68291 / 2.78 ( 1128) link_NAG-ASN : bond 0.00515 / 0.26 ( 4) link_NAG-ASN : angle 2.31748 / 1.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.094 Fit side-chains REVERT: A 115 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5796 (ptp) outliers start: 10 outliers final: 8 residues processed: 33 average time/residue: 0.0391 time to fit residues: 2.0204 Evaluate side-chains 36 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.173896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.130043 restraints weight = 4010.400| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.79 r_work: 0.3135 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4426 Z= 0.156 Angle : 0.512 6.742 6000 Z= 0.276 Chirality : 0.036 0.264 681 Planarity : 0.002 0.016 739 Dihedral : 5.125 51.440 676 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.25 % Allowed : 8.99 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.97 (0.35), residues: 532 helix: 3.49 (0.22), residues: 428 sheet: None (None), residues: 0 loop : -1.54 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 92 TYR 0.011 0.001 TYR B 257 PHE 0.014 0.001 PHE A 126 TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 4422) covalent geometry : angle 0.50271 / 0.27 ( 5988) hydrogen bonds : bond 0.03953 / 2.68 ( 376) hydrogen bonds : angle 3.76359 / 2.83 ( 1128) link_NAG-ASN : bond 0.00485 / 0.24 ( 4) link_NAG-ASN : angle 2.21459 / 1.28 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.144 Fit side-chains REVERT: A 115 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.6321 (ptp) outliers start: 10 outliers final: 8 residues processed: 30 average time/residue: 0.0402 time to fit residues: 1.9610 Evaluate side-chains 34 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.173471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127096 restraints weight = 4049.720| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.83 r_work: 0.3115 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4426 Z= 0.160 Angle : 0.516 7.067 6000 Z= 0.278 Chirality : 0.036 0.253 681 Planarity : 0.002 0.015 739 Dihedral : 5.150 51.328 676 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.02 % Allowed : 9.44 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.96 (0.35), residues: 532 helix: 3.49 (0.22), residues: 427 sheet: None (None), residues: 0 loop : -1.51 (0.60), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 92 TYR 0.011 0.001 TYR B 257 PHE 0.014 0.001 PHE A 126 TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 4422) covalent geometry : angle 0.50788 / 0.28 ( 5988) hydrogen bonds : bond 0.03984 / 2.70 ( 376) hydrogen bonds : angle 3.79158 / 2.85 ( 1128) link_NAG-ASN : bond 0.00442 / 0.22 ( 4) link_NAG-ASN : angle 2.06105 / 1.21 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1130.10 seconds wall clock time: 20 minutes 5.64 seconds (1205.64 seconds total)