Starting phenix.real_space_refine on Wed Sep 17 04:33:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwn_47258/09_2025/9dwn_47258.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwn_47258/09_2025/9dwn_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dwn_47258/09_2025/9dwn_47258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwn_47258/09_2025/9dwn_47258.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dwn_47258/09_2025/9dwn_47258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwn_47258/09_2025/9dwn_47258.map" } 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-2.0-5805/lib/python3.9/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, 30 Unusual residues: {' K': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 31 Unusual residues: {' K': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 1.21, per 1000 atoms: 0.28 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: 0.36 Conformation dependent library (CDL) restraints added in 194.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.11 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: 0.79 Time building geometry restraints manager: 0.49 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: 1.400 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.890 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:1.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 aren 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 covalent geometry : bond 0.00366 ( 4422) covalent geometry : angle 0.59431 ( 5988) hydrogen bonds : bond 0.10020 ( 376) hydrogen bonds : angle 4.89116 ( 1128) link_NAG-ASN : bond 0.01115 ( 4) link_NAG-ASN : angle 4.62833 ( 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 : 0.117 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 32 average time/residue: 0.0398 time to fit residues: 2.0031 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 : 0.135 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.9980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.173674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.131267 restraints weight = 3976.153| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.47 r_work: 0.3184 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4426 Z= 0.148 Angle : 0.557 11.320 6000 Z= 0.284 Chirality : 0.038 0.306 681 Planarity : 0.003 0.021 739 Dihedral : 8.566 85.960 676 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.67 % Allowed : 4.04 % Favored : 95.28 % 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 aren not related in a simple way. whole: 3.50 (0.35), residues: 532 helix: 3.24 (0.22), residues: 427 sheet: None (None), residues: 0 loop : -1.98 (0.58), residues: 105 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 covalent geometry : bond 0.00327 ( 4422) covalent geometry : angle 0.52986 ( 5988) hydrogen bonds : bond 0.04007 ( 376) hydrogen bonds : angle 3.80346 ( 1128) link_NAG-ASN : bond 0.00810 ( 4) link_NAG-ASN : angle 3.85139 ( 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 31 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 86 ILE cc_start: 0.7118 (tp) cc_final: 0.6903 (tp) outliers start: 3 outliers final: 2 residues processed: 29 average time/residue: 0.0396 time to fit residues: 1.8782 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 : 0.179 ------------------------------------------------------------------------------- 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: 1.9990 chunk 41 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.167322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.122461 restraints weight = 3981.357| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.74 r_work: 0.3067 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4426 Z= 0.192 Angle : 0.576 10.149 6000 Z= 0.300 Chirality : 0.039 0.305 681 Planarity : 0.003 0.018 739 Dihedral : 5.407 51.761 676 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.12 % Allowed : 5.62 % Favored : 93.26 % 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 aren not related in a simple way. whole: 3.44 (0.35), residues: 532 helix: 3.15 (0.22), residues: 428 sheet: None (None), residues: 0 loop : -1.82 (0.59), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.013 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 161 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 4422) covalent geometry : angle 0.54605 ( 5988) hydrogen bonds : bond 0.04243 ( 376) hydrogen bonds : angle 3.92396 ( 1128) link_NAG-ASN : bond 0.00826 ( 4) link_NAG-ASN : angle 4.16140 ( 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 35 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 86 ILE cc_start: 0.7459 (tp) cc_final: 0.7246 (tp) outliers start: 5 outliers final: 5 residues processed: 32 average time/residue: 0.0408 time to fit residues: 2.0216 Evaluate side-chains 33 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR 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: 0.7980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.170956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125136 restraints weight = 3933.967| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.88 r_work: 0.3087 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1386 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= 0.141 Angle : 0.502 8.932 6000 Z= 0.267 Chirality : 0.036 0.308 681 Planarity : 0.002 0.018 739 Dihedral : 5.116 51.920 676 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.35 % Allowed : 7.64 % Favored : 91.01 % 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 aren not related in a simple way. whole: 3.72 (0.35), residues: 532 helix: 3.29 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.65 (0.60), residues: 101 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 covalent geometry : bond 0.00307 ( 4422) covalent geometry : angle 0.47918 ( 5988) hydrogen bonds : bond 0.03939 ( 376) hydrogen bonds : angle 3.73569 ( 1128) link_NAG-ASN : bond 0.00697 ( 4) link_NAG-ASN : angle 3.35581 ( 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 29 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.159 Fit side-chains REVERT: A 115 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6037 (ptp) REVERT: A 248 ASN cc_start: 0.7891 (p0) cc_final: 0.7482 (p0) outliers start: 6 outliers final: 4 residues processed: 26 average time/residue: 0.0423 time to fit residues: 1.7130 Evaluate side-chains 28 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.169983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.124130 restraints weight = 3930.694| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.85 r_work: 0.3093 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4426 Z= 0.153 Angle : 0.502 8.308 6000 Z= 0.270 Chirality : 0.037 0.303 681 Planarity : 0.002 0.017 739 Dihedral : 5.068 51.665 676 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.57 % Allowed : 8.54 % 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 aren not related in a simple way. whole: 3.82 (0.35), residues: 532 helix: 3.35 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.52 (0.60), residues: 101 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 covalent geometry : bond 0.00342 ( 4422) covalent geometry : angle 0.48368 ( 5988) hydrogen bonds : bond 0.03968 ( 376) hydrogen bonds : angle 3.74298 ( 1128) link_NAG-ASN : bond 0.00632 ( 4) link_NAG-ASN : angle 3.07984 ( 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 30 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.155 Fit side-chains REVERT: A 115 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6201 (ptp) REVERT: A 248 ASN cc_start: 0.7943 (p0) cc_final: 0.7540 (p0) outliers start: 7 outliers final: 5 residues processed: 26 average time/residue: 0.0435 time to fit residues: 1.8344 Evaluate side-chains 29 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 0.0010 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.170768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125890 restraints weight = 4005.966| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.86 r_work: 0.3121 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4426 Z= 0.145 Angle : 0.492 7.663 6000 Z= 0.265 Chirality : 0.036 0.293 681 Planarity : 0.002 0.018 739 Dihedral : 5.021 51.463 676 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.80 % Allowed : 8.76 % Favored : 89.44 % 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 aren not related in a simple way. whole: 3.92 (0.35), residues: 532 helix: 3.40 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.42 (0.62), residues: 101 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 covalent geometry : bond 0.00322 ( 4422) covalent geometry : angle 0.47604 ( 5988) hydrogen bonds : bond 0.03912 ( 376) hydrogen bonds : angle 3.70027 ( 1128) link_NAG-ASN : bond 0.00585 ( 4) link_NAG-ASN : angle 2.80787 ( 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 32 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.159 Fit side-chains REVERT: A 115 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6309 (ptp) REVERT: A 248 ASN cc_start: 0.7983 (p0) cc_final: 0.7573 (p0) outliers start: 8 outliers final: 6 residues processed: 28 average time/residue: 0.0418 time to fit residues: 1.8962 Evaluate side-chains 30 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 52 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.171346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.125198 restraints weight = 3969.428| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.93 r_work: 0.3064 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1519 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= 0.143 Angle : 0.486 7.390 6000 Z= 0.263 Chirality : 0.036 0.299 681 Planarity : 0.002 0.017 739 Dihedral : 5.000 51.513 676 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.80 % Allowed : 8.76 % Favored : 89.44 % 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 aren not related in a simple way. whole: 3.93 (0.35), residues: 532 helix: 3.42 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.47 (0.61), residues: 101 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 covalent geometry : bond 0.00316 ( 4422) covalent geometry : angle 0.47109 ( 5988) hydrogen bonds : bond 0.03889 ( 376) hydrogen bonds : angle 3.69378 ( 1128) link_NAG-ASN : bond 0.00591 ( 4) link_NAG-ASN : angle 2.69891 ( 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 30 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.159 Fit side-chains REVERT: A 115 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6062 (ptp) outliers start: 8 outliers final: 7 residues processed: 27 average time/residue: 0.0398 time to fit residues: 1.8575 Evaluate side-chains 30 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.172712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.127352 restraints weight = 3947.630| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.55 r_work: 0.3088 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4426 Z= 0.157 Angle : 0.498 6.812 6000 Z= 0.270 Chirality : 0.037 0.281 681 Planarity : 0.002 0.018 739 Dihedral : 5.056 51.432 676 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.80 % Allowed : 9.21 % Favored : 88.99 % 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 aren not related in a simple way. whole: 3.89 (0.35), residues: 532 helix: 3.39 (0.22), residues: 430 sheet: None (None), residues: 0 loop : -1.42 (0.62), residues: 102 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 B 64 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4422) covalent geometry : angle 0.48553 ( 5988) hydrogen bonds : bond 0.03976 ( 376) hydrogen bonds : angle 3.75003 ( 1128) link_NAG-ASN : bond 0.00532 ( 4) link_NAG-ASN : angle 2.50470 ( 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 36 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.152 Fit side-chains REVERT: A 115 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6339 (ptp) REVERT: A 248 ASN cc_start: 0.7901 (p0) cc_final: 0.7590 (p0) outliers start: 8 outliers final: 7 residues processed: 33 average time/residue: 0.0427 time to fit residues: 2.2211 Evaluate side-chains 35 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.174500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.129020 restraints weight = 3958.299| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.75 r_work: 0.3103 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1570 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= 0.139 Angle : 0.479 6.768 6000 Z= 0.260 Chirality : 0.036 0.273 681 Planarity : 0.002 0.018 739 Dihedral : 4.993 51.708 676 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.57 % Allowed : 10.11 % Favored : 88.31 % 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 aren not related in a simple way. whole: 4.00 (0.35), residues: 532 helix: 3.47 (0.22), residues: 430 sheet: None (None), residues: 0 loop : -1.39 (0.62), residues: 102 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 covalent geometry : bond 0.00306 ( 4422) covalent geometry : angle 0.46815 ( 5988) hydrogen bonds : bond 0.03861 ( 376) hydrogen bonds : angle 3.67662 ( 1128) link_NAG-ASN : bond 0.00509 ( 4) link_NAG-ASN : angle 2.34304 ( 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 30 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.154 Fit side-chains REVERT: A 115 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6227 (ptp) REVERT: A 248 ASN cc_start: 0.7844 (p0) cc_final: 0.7432 (p0) outliers start: 7 outliers final: 6 residues processed: 27 average time/residue: 0.0428 time to fit residues: 1.8980 Evaluate side-chains 30 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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 256 LEU Chi-restraints excluded: chain B residue 91 VAL 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: 0.9980 chunk 50 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 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: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.173211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127889 restraints weight = 3956.559| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.91 r_work: 0.3074 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4426 Z= 0.155 Angle : 0.495 6.740 6000 Z= 0.269 Chirality : 0.036 0.266 681 Planarity : 0.002 0.018 739 Dihedral : 5.038 51.396 676 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.57 % Allowed : 10.11 % Favored : 88.31 % 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 aren not related in a simple way. whole: 3.93 (0.35), residues: 532 helix: 3.42 (0.22), residues: 430 sheet: None (None), residues: 0 loop : -1.44 (0.62), residues: 102 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 0.003 0.001 TRP A 95 HIS 0.001 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 4422) covalent geometry : angle 0.48550 ( 5988) hydrogen bonds : bond 0.03956 ( 376) hydrogen bonds : angle 3.73804 ( 1128) link_NAG-ASN : bond 0.00475 ( 4) link_NAG-ASN : angle 2.24653 ( 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 30 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.140 Fit side-chains REVERT: A 115 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6235 (ptp) REVERT: A 248 ASN cc_start: 0.7806 (p0) cc_final: 0.7390 (p0) outliers start: 7 outliers final: 6 residues processed: 27 average time/residue: 0.0365 time to fit residues: 1.6447 Evaluate side-chains 30 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 256 LEU Chi-restraints excluded: chain B residue 91 VAL 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: 0.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 16 optimal weight: 0.0270 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.175877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.130692 restraints weight = 3984.626| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.94 r_work: 0.3121 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4426 Z= 0.126 Angle : 0.462 6.739 6000 Z= 0.252 Chirality : 0.035 0.254 681 Planarity : 0.002 0.018 739 Dihedral : 4.928 51.796 676 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.57 % Allowed : 10.34 % Favored : 88.09 % 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 aren not related in a simple way. whole: 4.08 (0.35), residues: 532 helix: 3.54 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.49 (0.61), residues: 101 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 covalent geometry : bond 0.00270 ( 4422) covalent geometry : angle 0.45355 ( 5988) hydrogen bonds : bond 0.03767 ( 376) hydrogen bonds : angle 3.61234 ( 1128) link_NAG-ASN : bond 0.00457 ( 4) link_NAG-ASN : angle 2.07242 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1286.03 seconds wall clock time: 22 minutes 46.24 seconds (1366.24 seconds total)