Starting phenix.real_space_refine on Fri May 9 23:35:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwn_47258/05_2025/9dwn_47258.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwn_47258/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dwn_47258/05_2025/9dwn_47258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwn_47258/05_2025/9dwn_47258.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwn_47258/05_2025/9dwn_47258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwn_47258/05_2025/9dwn_47258.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 3.36, per 1000 atoms: 0.78 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: 1.10 Conformation dependent library (CDL) restraints added in 512.5 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: 0.34 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: 1.27 Time building geometry restraints manager: 1.29 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 297 or \ resid 401 through 404)) selection = (chain 'B' and (resid 14 through 297 or resid 401 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: 0.760 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.930 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 64 PHE 0.015 0.001 PHE A 126 TYR 0.018 0.002 TYR A 102 ARG 0.003 0.000 ARG A 94 Details of bonding type rmsd link_NAG-ASN : bond 0.01115 ( 4) link_NAG-ASN : angle 4.62833 ( 12) hydrogen bonds : bond 0.10020 ( 376) hydrogen bonds : angle 4.89116 ( 1128) covalent geometry : bond 0.00366 ( 4422) covalent geometry : angle 0.59431 ( 5988) *********************** 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 : 0.456 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 32 average time/residue: 0.1018 time to fit residues: 5.1246 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 : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.170800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.125004 restraints weight = 3966.664| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.75 r_work: 0.3068 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4426 Z= 0.171 Angle : 0.579 11.090 6000 Z= 0.296 Chirality : 0.039 0.307 681 Planarity : 0.003 0.021 739 Dihedral : 8.468 82.843 676 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.90 % Allowed : 3.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.34), residues: 532 helix: 3.11 (0.22), residues: 428 sheet: None (None), residues: 0 loop : -1.94 (0.57), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 190 HIS 0.002 0.000 HIS A 64 PHE 0.016 0.002 PHE A 97 TYR 0.014 0.001 TYR B 257 ARG 0.002 0.000 ARG B 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00786 ( 4) link_NAG-ASN : angle 3.89238 ( 12) hydrogen bonds : bond 0.04132 ( 376) hydrogen bonds : angle 3.88148 ( 1128) covalent geometry : bond 0.00389 ( 4422) covalent geometry : angle 0.55232 ( 5988) *********************** 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: 4 poor density : 27 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 86 ILE cc_start: 0.7226 (tp) cc_final: 0.7026 (tp) REVERT: A 132 LEU cc_start: 0.8549 (tp) cc_final: 0.8346 (tp) outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.0962 time to fit residues: 4.5616 Evaluate side-chains 29 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain B residue 91 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.168000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.119828 restraints weight = 3926.056| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.88 r_work: 0.3008 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4426 Z= 0.187 Angle : 0.561 9.429 6000 Z= 0.296 Chirality : 0.038 0.304 681 Planarity : 0.003 0.019 739 Dihedral : 5.328 51.795 676 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.90 % Allowed : 6.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.35), residues: 532 helix: 3.12 (0.22), residues: 429 sheet: None (None), residues: 0 loop : -1.80 (0.60), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 190 HIS 0.001 0.000 HIS B 64 PHE 0.015 0.002 PHE A 126 TYR 0.013 0.001 TYR B 257 ARG 0.003 0.000 ARG B 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00723 ( 4) link_NAG-ASN : angle 3.83390 ( 12) hydrogen bonds : bond 0.04205 ( 376) hydrogen bonds : angle 3.91147 ( 1128) covalent geometry : bond 0.00433 ( 4422) covalent geometry : angle 0.53493 ( 5988) *********************** 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 32 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.420 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 29 average time/residue: 0.0968 time to fit residues: 4.5121 Evaluate side-chains 30 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 256 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.169033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.121521 restraints weight = 3984.632| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.71 r_work: 0.3064 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1494 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= 0.161 Angle : 0.518 8.688 6000 Z= 0.276 Chirality : 0.037 0.307 681 Planarity : 0.002 0.019 739 Dihedral : 5.146 51.225 676 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.35), residues: 532 helix: 3.23 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.51 (0.62), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 64 PHE 0.015 0.001 PHE A 126 TYR 0.012 0.001 TYR B 257 ARG 0.002 0.000 ARG B 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00649 ( 4) link_NAG-ASN : angle 3.23763 ( 12) hydrogen bonds : bond 0.04037 ( 376) hydrogen bonds : angle 3.80347 ( 1128) covalent geometry : bond 0.00364 ( 4422) covalent geometry : angle 0.49772 ( 5988) *********************** 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 31 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.537 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 27 average time/residue: 0.1019 time to fit residues: 4.4892 Evaluate side-chains 28 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 0.0770 chunk 49 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.170909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124902 restraints weight = 3970.198| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.90 r_work: 0.3091 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1453 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= 0.140 Angle : 0.488 7.850 6000 Z= 0.263 Chirality : 0.036 0.297 681 Planarity : 0.002 0.019 739 Dihedral : 5.036 51.480 676 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.80 % Allowed : 7.87 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.35), residues: 532 helix: 3.37 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.29 (0.63), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 64 PHE 0.014 0.001 PHE A 126 TYR 0.011 0.001 TYR B 257 ARG 0.002 0.000 ARG B 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 4) link_NAG-ASN : angle 2.90306 ( 12) hydrogen bonds : bond 0.03896 ( 376) hydrogen bonds : angle 3.68360 ( 1128) covalent geometry : bond 0.00307 ( 4422) covalent geometry : angle 0.47111 ( 5988) *********************** 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 29 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.418 Fit side-chains REVERT: A 115 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6239 (ptp) outliers start: 8 outliers final: 5 residues processed: 25 average time/residue: 0.1009 time to fit residues: 4.0811 Evaluate side-chains 26 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 35 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.168597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.123669 restraints weight = 3977.623| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.88 r_work: 0.3060 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4426 Z= 0.172 Angle : 0.517 7.433 6000 Z= 0.279 Chirality : 0.037 0.293 681 Planarity : 0.002 0.020 739 Dihedral : 5.084 50.406 676 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.57 % Allowed : 8.76 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.35), residues: 532 helix: 3.30 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.36 (0.62), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 53 HIS 0.001 0.000 HIS A 64 PHE 0.014 0.002 PHE A 126 TYR 0.011 0.001 TYR A 257 ARG 0.002 0.000 ARG B 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 4) link_NAG-ASN : angle 2.74971 ( 12) hydrogen bonds : bond 0.04067 ( 376) hydrogen bonds : angle 3.79730 ( 1128) covalent geometry : bond 0.00394 ( 4422) covalent geometry : angle 0.50221 ( 5988) *********************** 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: 7 poor density : 25 time to evaluate : 0.482 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 29 average time/residue: 0.1001 time to fit residues: 4.6855 Evaluate side-chains 30 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 0.0070 chunk 3 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 46 optimal weight: 0.0470 chunk 30 optimal weight: 0.9980 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.173451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.128047 restraints weight = 3928.753| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.90 r_work: 0.3129 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4426 Z= 0.123 Angle : 0.465 6.865 6000 Z= 0.252 Chirality : 0.035 0.279 681 Planarity : 0.002 0.019 739 Dihedral : 4.942 51.384 676 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.35 % Allowed : 9.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.09 (0.35), residues: 532 helix: 3.50 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.22 (0.63), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 289 HIS 0.001 0.000 HIS A 64 PHE 0.014 0.001 PHE A 126 TYR 0.011 0.001 TYR A 78 ARG 0.001 0.000 ARG A 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 4) link_NAG-ASN : angle 2.44941 ( 12) hydrogen bonds : bond 0.03766 ( 376) hydrogen bonds : angle 3.60019 ( 1128) covalent geometry : bond 0.00259 ( 4422) covalent geometry : angle 0.45207 ( 5988) *********************** 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 29 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.451 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 28 average time/residue: 0.1036 time to fit residues: 4.7627 Evaluate side-chains 28 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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 41 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.169327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.123278 restraints weight = 3919.446| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.88 r_work: 0.3045 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4426 Z= 0.161 Angle : 0.501 6.787 6000 Z= 0.272 Chirality : 0.037 0.285 681 Planarity : 0.002 0.019 739 Dihedral : 5.032 50.985 676 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.57 % Allowed : 9.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.95 (0.35), residues: 532 helix: 3.40 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.26 (0.64), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 53 HIS 0.001 0.000 HIS A 64 PHE 0.014 0.001 PHE A 126 TYR 0.011 0.001 TYR B 257 ARG 0.001 0.000 ARG B 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 4) link_NAG-ASN : angle 2.46741 ( 12) hydrogen bonds : bond 0.03988 ( 376) hydrogen bonds : angle 3.74365 ( 1128) covalent geometry : bond 0.00363 ( 4422) covalent geometry : angle 0.48904 ( 5988) *********************** 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: 7 poor density : 28 time to evaluate : 0.425 Fit side-chains REVERT: A 115 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6058 (ptp) outliers start: 7 outliers final: 6 residues processed: 32 average time/residue: 0.0973 time to fit residues: 4.9796 Evaluate side-chains 35 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.174054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.126882 restraints weight = 3978.149| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.84 r_work: 0.3055 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4426 Z= 0.159 Angle : 0.500 6.732 6000 Z= 0.271 Chirality : 0.037 0.288 681 Planarity : 0.002 0.019 739 Dihedral : 5.065 51.249 676 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.47 % Allowed : 9.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.35), residues: 532 helix: 3.40 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.30 (0.63), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 190 HIS 0.001 0.000 HIS A 64 PHE 0.014 0.001 PHE A 126 TYR 0.011 0.001 TYR B 257 ARG 0.001 0.000 ARG B 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 4) link_NAG-ASN : angle 2.45365 ( 12) hydrogen bonds : bond 0.03979 ( 376) hydrogen bonds : angle 3.74212 ( 1128) covalent geometry : bond 0.00358 ( 4422) covalent geometry : angle 0.48797 ( 5988) *********************** 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 32 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.457 Fit side-chains REVERT: A 115 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6052 (ptp) outliers start: 11 outliers final: 8 residues processed: 28 average time/residue: 0.0987 time to fit residues: 4.5198 Evaluate side-chains 30 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 198 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 0.0060 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.173954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.127988 restraints weight = 3863.094| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.79 r_work: 0.3077 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4426 Z= 0.142 Angle : 0.482 6.700 6000 Z= 0.262 Chirality : 0.036 0.266 681 Planarity : 0.002 0.018 739 Dihedral : 5.012 51.350 676 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.02 % Allowed : 9.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.02 (0.35), residues: 532 helix: 3.45 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.27 (0.63), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 64 PHE 0.014 0.001 PHE A 126 TYR 0.011 0.001 TYR B 257 ARG 0.001 0.000 ARG B 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 4) link_NAG-ASN : angle 2.23485 ( 12) hydrogen bonds : bond 0.03876 ( 376) hydrogen bonds : angle 3.69017 ( 1128) covalent geometry : bond 0.00313 ( 4422) covalent geometry : angle 0.47157 ( 5988) ********************** 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 31 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.464 Fit side-chains REVERT: A 115 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6161 (ptp) outliers start: 9 outliers final: 8 residues processed: 27 average time/residue: 0.1029 time to fit residues: 4.5496 Evaluate side-chains 30 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 198 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 0.0870 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.172255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.126518 restraints weight = 3905.754| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.80 r_work: 0.3094 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4426 Z= 0.133 Angle : 0.470 6.715 6000 Z= 0.257 Chirality : 0.035 0.255 681 Planarity : 0.002 0.018 739 Dihedral : 4.964 51.689 676 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.80 % Allowed : 9.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.35), residues: 532 helix: 3.52 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.26 (0.63), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 64 PHE 0.014 0.001 PHE A 126 TYR 0.011 0.001 TYR A 78 ARG 0.001 0.000 ARG A 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 4) link_NAG-ASN : angle 2.08657 ( 12) hydrogen bonds : bond 0.03789 ( 376) hydrogen bonds : angle 3.63579 ( 1128) covalent geometry : bond 0.00291 ( 4422) covalent geometry : angle 0.46134 ( 5988) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2393.67 seconds wall clock time: 42 minutes 7.98 seconds (2527.98 seconds total)