Starting phenix.real_space_refine on Sun Apr 27 02:44:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwn_47258/04_2025/9dwn_47258.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwn_47258/04_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_47258/04_2025/9dwn_47258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwn_47258/04_2025/9dwn_47258.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwn_47258/04_2025/9dwn_47258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwn_47258/04_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-5669/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: 3.31, per 1000 atoms: 0.77 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: 2.35 Conformation dependent library (CDL) restraints added in 703.2 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: 0.29 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: 1.13 Time building geometry restraints manager: 1.27 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: 0.920 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.570 Find NCS groups from input model: 0.170 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.830 ------------------------------------------------------------------------------- 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 : 0.474 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 32 average time/residue: 0.1024 time to fit residues: 5.1730 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 : 0.446 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.170840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124643 restraints weight = 3967.056| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.78 r_work: 0.3060 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- 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 11.091 6000 Z= 0.296 Chirality : 0.039 0.307 681 Planarity : 0.003 0.021 739 Dihedral : 8.469 82.844 676 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 3.89237 ( 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 : 0.407 Fit side-chains revert: symmetry clash REVERT: A 86 ILE cc_start: 0.7223 (tp) cc_final: 0.7019 (tp) REVERT: A 132 LEU cc_start: 0.8545 (tp) cc_final: 0.8344 (tp) outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.0976 time to fit residues: 4.6455 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 : 0.432 ------------------------------------------------------------------------------- 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: 0.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.167784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.120313 restraints weight = 3923.321| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.89 r_work: 0.3014 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4426 Z= 0.188 Angle : 0.563 9.418 6000 Z= 0.297 Chirality : 0.038 0.305 681 Planarity : 0.003 0.019 739 Dihedral : 5.327 51.794 676 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.12 % Allowed : 6.07 % Favored : 92.81 % 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: 3.42 (0.35), residues: 532 helix: 3.10 (0.22), residues: 430 sheet: None (None), residues: 0 loop : -1.79 (0.60), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 190 HIS 0.001 0.000 HIS A 161 PHE 0.015 0.002 PHE A 126 TYR 0.013 0.001 TYR B 257 ARG 0.002 0.000 ARG B 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00709 ( 4) link_NAG-ASN : angle 3.82930 ( 12) hydrogen bonds : bond 0.04213 ( 376) hydrogen bonds : angle 3.91361 ( 1128) covalent geometry : bond 0.00434 ( 4422) covalent geometry : angle 0.53729 ( 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 34 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 86 ILE cc_start: 0.7342 (tp) cc_final: 0.7141 (tp) outliers start: 5 outliers final: 5 residues processed: 31 average time/residue: 0.1450 time to fit residues: 7.2609 Evaluate side-chains 31 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 190 TRP 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: 9.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.168938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.123698 restraints weight = 3983.677| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.75 r_work: 0.3090 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1507 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= 0.164 Angle : 0.522 8.747 6000 Z= 0.278 Chirality : 0.037 0.309 681 Planarity : 0.002 0.020 739 Dihedral : 5.159 51.214 676 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.35 % Allowed : 7.87 % Favored : 90.79 % 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: 3.62 (0.35), residues: 532 helix: 3.20 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.58 (0.61), 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 0.00655 ( 4) link_NAG-ASN : angle 3.28585 ( 12) hydrogen bonds : bond 0.04061 ( 376) hydrogen bonds : angle 3.81956 ( 1128) covalent geometry : bond 0.00370 ( 4422) covalent geometry : angle 0.50089 ( 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 26 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 86 ILE cc_start: 0.7371 (tp) cc_final: 0.7156 (tp) outliers start: 6 outliers final: 5 residues processed: 23 average time/residue: 0.0999 time to fit residues: 3.7799 Evaluate side-chains 25 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 0.0470 chunk 49 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.171968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.126316 restraints weight = 3956.892| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.86 r_work: 0.3104 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4426 Z= 0.131 Angle : 0.479 7.812 6000 Z= 0.257 Chirality : 0.036 0.295 681 Planarity : 0.002 0.019 739 Dihedral : 4.998 51.730 676 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.35 % Allowed : 8.09 % 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: 3.95 (0.35), residues: 532 helix: 3.41 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.31 (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 0.00610 ( 4) link_NAG-ASN : angle 2.87889 ( 12) hydrogen bonds : bond 0.03835 ( 376) hydrogen bonds : angle 3.63115 ( 1128) covalent geometry : bond 0.00282 ( 4422) covalent geometry : angle 0.46177 ( 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 30 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.464 Fit side-chains REVERT: A 115 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6052 (ptp) outliers start: 6 outliers final: 3 residues processed: 26 average time/residue: 0.1031 time to fit residues: 4.4263 Evaluate side-chains 27 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 0.0770 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 37 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.173569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.128122 restraints weight = 3955.299| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.94 r_work: 0.3125 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1421 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= 0.124 Angle : 0.466 7.092 6000 Z= 0.252 Chirality : 0.035 0.283 681 Planarity : 0.002 0.019 739 Dihedral : 4.904 51.355 676 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.35 % Allowed : 8.76 % 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 (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: 4.12 (0.35), residues: 532 helix: 3.56 (0.22), residues: 429 sheet: None (None), residues: 0 loop : -1.32 (0.62), residues: 103 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 0.010 0.001 TYR A 78 ARG 0.001 0.000 ARG B 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 4) link_NAG-ASN : angle 2.60497 ( 12) hydrogen bonds : bond 0.03752 ( 376) hydrogen bonds : angle 3.58085 ( 1128) covalent geometry : bond 0.00263 ( 4422) covalent geometry : angle 0.45157 ( 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 31 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.455 Fit side-chains REVERT: A 115 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6012 (ptp) outliers start: 6 outliers final: 5 residues processed: 28 average time/residue: 0.1040 time to fit residues: 4.7531 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 : 0.472 ------------------------------------------------------------------------------- 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: 1.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.171106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.125209 restraints weight = 3940.215| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.86 r_work: 0.3088 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1515 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= 0.144 Angle : 0.485 6.895 6000 Z= 0.263 Chirality : 0.036 0.291 681 Planarity : 0.002 0.019 739 Dihedral : 4.965 51.123 676 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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 (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: 3.49 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.22 (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 A 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 4) link_NAG-ASN : angle 2.54929 ( 12) hydrogen bonds : bond 0.03877 ( 376) hydrogen bonds : angle 3.65267 ( 1128) covalent geometry : bond 0.00321 ( 4422) covalent geometry : angle 0.47167 ( 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 37 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.446 Fit side-chains REVERT: A 115 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6056 (ptp) outliers start: 8 outliers final: 6 residues processed: 32 average time/residue: 0.1027 time to fit residues: 5.2691 Evaluate side-chains 36 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 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: 5.9990 chunk 4 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.171978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.126139 restraints weight = 3899.458| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.91 r_work: 0.3099 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1524 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= 0.136 Angle : 0.475 6.772 6000 Z= 0.258 Chirality : 0.036 0.284 681 Planarity : 0.002 0.018 739 Dihedral : 4.960 51.765 676 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 : 10.11 % 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: 4.13 (0.35), residues: 532 helix: 3.53 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.20 (0.64), 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 0.010 0.001 TYR A 78 ARG 0.001 0.000 ARG B 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 4) link_NAG-ASN : angle 2.44998 ( 12) hydrogen bonds : bond 0.03834 ( 376) hydrogen bonds : angle 3.62267 ( 1128) covalent geometry : bond 0.00297 ( 4422) covalent geometry : angle 0.46305 ( 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 28 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.383 Fit side-chains REVERT: A 115 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6065 (ptp) outliers start: 6 outliers final: 5 residues processed: 25 average time/residue: 0.0985 time to fit residues: 4.0634 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 : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 91 VAL 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 46 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 50 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 0.0070 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.174278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129263 restraints weight = 3972.198| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.59 r_work: 0.3146 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 0.027 4426 Z= 0.128 Angle : 0.463 6.694 6000 Z= 0.252 Chirality : 0.035 0.261 681 Planarity : 0.002 0.019 739 Dihedral : 4.901 51.476 676 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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 (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: 4.21 (0.35), residues: 532 helix: 3.58 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.21 (0.64), 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 0.00494 ( 4) link_NAG-ASN : angle 2.21705 ( 12) hydrogen bonds : bond 0.03762 ( 376) hydrogen bonds : angle 3.58179 ( 1128) covalent geometry : bond 0.00275 ( 4422) covalent geometry : angle 0.45269 ( 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 30 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.503 Fit side-chains REVERT: A 115 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.6373 (ptp) outliers start: 7 outliers final: 6 residues processed: 27 average time/residue: 0.1032 time to fit residues: 4.6700 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 : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 198 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 40 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 45 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 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 = 0.3853 r_free = 0.3853 target = 0.174483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.126886 restraints weight = 3865.293| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.93 r_work: 0.3081 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1563 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= 0.138 Angle : 0.474 6.685 6000 Z= 0.258 Chirality : 0.036 0.258 681 Planarity : 0.002 0.019 739 Dihedral : 4.943 51.578 676 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.02 % Allowed : 9.66 % 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: 4.16 (0.35), residues: 532 helix: 3.55 (0.22), residues: 431 sheet: None (None), residues: 0 loop : -1.20 (0.64), 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 0.00463 ( 4) link_NAG-ASN : angle 2.11537 ( 12) hydrogen bonds : bond 0.03834 ( 376) hydrogen bonds : angle 3.62430 ( 1128) covalent geometry : bond 0.00302 ( 4422) covalent geometry : angle 0.46481 ( 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 36 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.411 Fit side-chains REVERT: A 115 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6076 (ptp) outliers start: 9 outliers final: 5 residues processed: 32 average time/residue: 0.0977 time to fit residues: 5.0602 Evaluate side-chains 32 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 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 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.174465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.126496 restraints weight = 3911.121| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.91 r_work: 0.3063 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4426 Z= 0.145 Angle : 0.481 6.691 6000 Z= 0.263 Chirality : 0.036 0.252 681 Planarity : 0.002 0.019 739 Dihedral : 4.975 51.336 676 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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 (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: 4.12 (0.35), residues: 532 helix: 3.52 (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 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 B 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 4) link_NAG-ASN : angle 2.03419 ( 12) hydrogen bonds : bond 0.03873 ( 376) hydrogen bonds : angle 3.66108 ( 1128) covalent geometry : bond 0.00323 ( 4422) covalent geometry : angle 0.47247 ( 5988) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2518.36 seconds wall clock time: 44 minutes 35.68 seconds (2675.68 seconds total)