Starting phenix.real_space_refine on Wed Jul 23 17:32:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5l_10701/07_2025/6y5l_10701.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5l_10701/07_2025/6y5l_10701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6y5l_10701/07_2025/6y5l_10701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5l_10701/07_2025/6y5l_10701.map" model { file = "/net/cci-nas-00/data/ceres_data/6y5l_10701/07_2025/6y5l_10701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5l_10701/07_2025/6y5l_10701.cif" } resolution = 3.6 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= 0.004 sd= 0.140 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2403 2.51 5 N 654 2.21 5 O 786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3855 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 531 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain breaks: 1 Chain: "B" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 740 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, E, D, F Time building chain proxies: 3.69, per 1000 atoms: 0.96 Number of scatterers: 3855 At special positions: 0 Unit cell: (68.481, 71.742, 147.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 786 8.00 N 654 7.00 C 2403 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 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 38 " " NAG C 401 " - " ASN C 38 " " NAG E 401 " - " ASN E 38 " Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 572.6 milliseconds 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 9 sheets defined 55.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 38 through 125 Processing helix chain 'D' and resid 38 through 125 Processing helix chain 'F' and resid 38 through 125 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA4, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AA5, first strand: chain 'C' and resid 282 through 283 Processing sheet with id=AA6, first strand: chain 'C' and resid 294 through 295 Processing sheet with id=AA7, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AA8, first strand: chain 'E' and resid 282 through 283 Processing sheet with id=AA9, first strand: chain 'E' and resid 294 through 295 273 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 1.19 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: 1270 1.34 - 1.46: 370 1.46 - 1.57: 2242 1.57 - 1.69: 0 1.69 - 1.80: 18 Bond restraints: 3900 Sorted by residual: bond pdb=" C1 NAG C 401 " pdb=" O5 NAG C 401 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.72e+00 bond pdb=" C1 NAG E 401 " pdb=" O5 NAG E 401 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" C1 NAG A 401 " pdb=" O5 NAG A 401 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.69e+00 bond pdb=" C5 NAG E 401 " pdb=" O5 NAG E 401 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.27e+00 bond pdb=" C5 NAG C 401 " pdb=" O5 NAG C 401 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.24e+00 ... (remaining 3895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 4959 1.37 - 2.73: 272 2.73 - 4.10: 37 4.10 - 5.46: 0 5.46 - 6.83: 3 Bond angle restraints: 5271 Sorted by residual: angle pdb=" N ILE E 29 " pdb=" CA ILE E 29 " pdb=" C ILE E 29 " ideal model delta sigma weight residual 112.96 110.20 2.76 1.00e+00 1.00e+00 7.60e+00 angle pdb=" N ILE C 29 " pdb=" CA ILE C 29 " pdb=" C ILE C 29 " ideal model delta sigma weight residual 112.96 110.22 2.74 1.00e+00 1.00e+00 7.50e+00 angle pdb=" N ILE A 29 " pdb=" CA ILE A 29 " pdb=" C ILE A 29 " ideal model delta sigma weight residual 112.96 110.23 2.73 1.00e+00 1.00e+00 7.47e+00 angle pdb=" N ALA E 317 " pdb=" CA ALA E 317 " pdb=" C ALA E 317 " ideal model delta sigma weight residual 110.42 114.10 -3.68 1.46e+00 4.69e-01 6.35e+00 angle pdb=" N ALA A 317 " pdb=" CA ALA A 317 " pdb=" C ALA A 317 " ideal model delta sigma weight residual 110.42 114.05 -3.63 1.46e+00 4.69e-01 6.18e+00 ... (remaining 5266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2214 17.34 - 34.67: 204 34.67 - 52.01: 48 52.01 - 69.35: 6 69.35 - 86.69: 3 Dihedral angle restraints: 2475 sinusoidal: 1077 harmonic: 1398 Sorted by residual: dihedral pdb=" CA PRO C 306 " pdb=" C PRO C 306 " pdb=" N LYS C 307 " pdb=" CA LYS C 307 " ideal model delta harmonic sigma weight residual -180.00 -163.72 -16.28 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA PRO A 306 " pdb=" C PRO A 306 " pdb=" N LYS A 307 " pdb=" CA LYS A 307 " ideal model delta harmonic sigma weight residual -180.00 -163.76 -16.24 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA PRO E 306 " pdb=" C PRO E 306 " pdb=" N LYS E 307 " pdb=" CA LYS E 307 " ideal model delta harmonic sigma weight residual -180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 343 0.028 - 0.057: 154 0.057 - 0.085: 64 0.085 - 0.113: 40 0.113 - 0.141: 26 Chirality restraints: 627 Sorted by residual: chirality pdb=" CA ASP F 46 " pdb=" N ASP F 46 " pdb=" C ASP F 46 " pdb=" CB ASP F 46 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ASP B 46 " pdb=" N ASP B 46 " pdb=" C ASP B 46 " pdb=" CB ASP B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ASP D 46 " pdb=" N ASP D 46 " pdb=" C ASP D 46 " pdb=" CB ASP D 46 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 624 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 46 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" CG ASP B 46 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP B 46 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP B 46 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 46 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.43e+00 pdb=" CG ASP F 46 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP F 46 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP F 46 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 46 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" CG ASP D 46 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP D 46 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP D 46 " 0.016 2.00e-02 2.50e+03 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 163 2.71 - 3.26: 4084 3.26 - 3.80: 5948 3.80 - 4.35: 6904 4.35 - 4.90: 11814 Nonbonded interactions: 28913 Sorted by model distance: nonbonded pdb=" NZ LYS A 27 " pdb=" OE2 GLU B 97 " model vdw 2.161 3.120 nonbonded pdb=" NZ LYS E 27 " pdb=" OE2 GLU F 97 " model vdw 2.259 3.120 nonbonded pdb=" NZ LYS C 27 " pdb=" OE2 GLU D 97 " model vdw 2.388 3.120 nonbonded pdb=" O LEU D 38 " pdb=" OG1 THR D 41 " model vdw 2.400 3.040 nonbonded pdb=" O LEU B 38 " pdb=" OG1 THR B 41 " model vdw 2.400 3.040 ... (remaining 28908 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.510 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 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 0.032 3906 Z= 0.174 Angle : 0.704 6.830 5286 Z= 0.402 Chirality : 0.048 0.141 627 Planarity : 0.006 0.051 684 Dihedral : 14.311 86.685 1548 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % 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: -2.14 (0.34), residues: 459 helix: 0.80 (0.25), residues: 261 sheet: -4.11 (0.66), residues: 30 loop : -4.75 (0.34), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 92 HIS 0.005 0.002 HIS F 64 PHE 0.023 0.003 PHE D 63 TYR 0.022 0.003 TYR E 308 ARG 0.002 0.000 ARG F 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 3) link_NAG-ASN : angle 1.40889 ( 9) hydrogen bonds : bond 0.08119 ( 273) hydrogen bonds : angle 4.50729 ( 792) SS BOND : bond 0.00126 ( 3) SS BOND : angle 1.19134 ( 6) covalent geometry : bond 0.00352 ( 3900) covalent geometry : angle 0.70143 ( 5271) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7659 (mmmt) cc_final: 0.7178 (mtpp) REVERT: B 51 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8788 (ptpp) REVERT: B 54 ARG cc_start: 0.8310 (mtp85) cc_final: 0.7903 (ttm110) REVERT: B 110 LEU cc_start: 0.9037 (mt) cc_final: 0.8639 (mt) REVERT: B 121 LYS cc_start: 0.9238 (mtpt) cc_final: 0.9020 (tmtt) REVERT: C 307 LYS cc_start: 0.7251 (mmmt) cc_final: 0.6919 (mtpp) REVERT: E 307 LYS cc_start: 0.7392 (mmmt) cc_final: 0.7108 (mtpp) REVERT: E 320 MET cc_start: 0.6638 (ttm) cc_final: 0.5879 (ttm) REVERT: D 51 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8650 (ptpp) REVERT: D 54 ARG cc_start: 0.8365 (mtp85) cc_final: 0.8128 (ttm110) REVERT: D 58 LYS cc_start: 0.8887 (mttt) cc_final: 0.8652 (mttm) REVERT: D 110 LEU cc_start: 0.9188 (mt) cc_final: 0.8738 (mt) REVERT: F 54 ARG cc_start: 0.8435 (mtp85) cc_final: 0.8197 (ttm110) REVERT: F 64 HIS cc_start: 0.7756 (m-70) cc_final: 0.7452 (m-70) REVERT: F 112 ASP cc_start: 0.8912 (p0) cc_final: 0.8608 (p0) REVERT: F 121 LYS cc_start: 0.9208 (mtpt) cc_final: 0.8890 (tptp) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2051 time to fit residues: 49.5683 Evaluate side-chains 163 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.4980 chunk 34 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 322 ASN B 60 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 322 ASN E 296 ASN E 322 ASN D 60 ASN D 78 GLN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN F 60 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.131442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.090443 restraints weight = 6889.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.092887 restraints weight = 4570.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.094357 restraints weight = 3642.944| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3906 Z= 0.186 Angle : 0.691 4.689 5286 Z= 0.373 Chirality : 0.047 0.153 627 Planarity : 0.006 0.041 684 Dihedral : 5.172 37.041 561 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.99 % Allowed : 19.08 % Favored : 77.93 % 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: -0.35 (0.38), residues: 459 helix: 2.57 (0.26), residues: 261 sheet: -4.22 (0.46), residues: 30 loop : -4.37 (0.37), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 92 HIS 0.010 0.002 HIS B 106 PHE 0.015 0.002 PHE D 70 TYR 0.014 0.003 TYR C 302 ARG 0.004 0.001 ARG F 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 3) link_NAG-ASN : angle 2.28373 ( 9) hydrogen bonds : bond 0.03322 ( 273) hydrogen bonds : angle 3.62950 ( 792) SS BOND : bond 0.00523 ( 3) SS BOND : angle 2.07558 ( 6) covalent geometry : bond 0.00426 ( 3900) covalent geometry : angle 0.68159 ( 5271) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7824 (mmmt) cc_final: 0.7418 (mtpp) REVERT: A 320 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.5547 (ttm) REVERT: B 51 LYS cc_start: 0.9260 (mmtt) cc_final: 0.8854 (ptpp) REVERT: B 58 LYS cc_start: 0.9116 (mttp) cc_final: 0.8864 (mmtp) REVERT: B 64 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7468 (t-90) REVERT: B 110 LEU cc_start: 0.8956 (mt) cc_final: 0.8566 (mt) REVERT: B 112 ASP cc_start: 0.8748 (p0) cc_final: 0.8538 (p0) REVERT: B 121 LYS cc_start: 0.9318 (mtpt) cc_final: 0.9018 (tmtt) REVERT: C 41 GLU cc_start: 0.7950 (tp30) cc_final: 0.7704 (tp30) REVERT: C 307 LYS cc_start: 0.7551 (mmmt) cc_final: 0.7208 (mtpp) REVERT: E 22 ASN cc_start: 0.7063 (m-40) cc_final: 0.6462 (t0) REVERT: E 320 MET cc_start: 0.6775 (ttm) cc_final: 0.6475 (ttm) REVERT: D 51 LYS cc_start: 0.9287 (mmtt) cc_final: 0.8859 (ptpt) REVERT: D 54 ARG cc_start: 0.8666 (mtp85) cc_final: 0.8321 (ttp-110) REVERT: D 58 LYS cc_start: 0.9148 (mttt) cc_final: 0.8791 (mttm) REVERT: D 110 LEU cc_start: 0.9131 (mt) cc_final: 0.8928 (mt) REVERT: F 51 LYS cc_start: 0.9380 (mmtt) cc_final: 0.9005 (ptpt) REVERT: F 54 ARG cc_start: 0.8836 (mtp85) cc_final: 0.8425 (ttm110) REVERT: F 58 LYS cc_start: 0.9169 (mttt) cc_final: 0.8889 (mmtt) REVERT: F 64 HIS cc_start: 0.8274 (m-70) cc_final: 0.7827 (m-70) REVERT: F 121 LYS cc_start: 0.9265 (mtpt) cc_final: 0.8980 (tptp) outliers start: 13 outliers final: 5 residues processed: 171 average time/residue: 0.1916 time to fit residues: 38.8961 Evaluate side-chains 161 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 64 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 3 optimal weight: 0.5980 chunk 21 optimal weight: 0.0010 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 296 ASN B 105 GLN C 322 ASN E 295 GLN E 296 ASN E 322 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.133310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.099243 restraints weight = 6929.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.099286 restraints weight = 6441.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.100374 restraints weight = 4865.302| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3906 Z= 0.145 Angle : 0.728 11.786 5286 Z= 0.391 Chirality : 0.045 0.152 627 Planarity : 0.006 0.047 684 Dihedral : 4.924 36.237 561 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.68 % Allowed : 19.54 % Favored : 76.78 % 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: 0.46 (0.40), residues: 459 helix: 3.27 (0.28), residues: 261 sheet: -4.19 (0.47), residues: 30 loop : -4.06 (0.38), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 92 HIS 0.011 0.003 HIS B 106 PHE 0.009 0.001 PHE D 70 TYR 0.008 0.002 TYR C 302 ARG 0.005 0.001 ARG F 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 3) link_NAG-ASN : angle 2.11289 ( 9) hydrogen bonds : bond 0.03332 ( 273) hydrogen bonds : angle 3.54043 ( 792) SS BOND : bond 0.00282 ( 3) SS BOND : angle 1.69183 ( 6) covalent geometry : bond 0.00319 ( 3900) covalent geometry : angle 0.72121 ( 5271) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7480 (mmmt) cc_final: 0.7023 (mtpp) REVERT: B 64 HIS cc_start: 0.8230 (m-70) cc_final: 0.7451 (t-90) REVERT: B 121 LYS cc_start: 0.9221 (mtpt) cc_final: 0.8978 (tmtt) REVERT: C 307 LYS cc_start: 0.7483 (mmmt) cc_final: 0.7207 (mtpp) REVERT: E 22 ASN cc_start: 0.6820 (m-40) cc_final: 0.6405 (t0) REVERT: E 320 MET cc_start: 0.6650 (ttm) cc_final: 0.6339 (ttm) REVERT: D 58 LYS cc_start: 0.9008 (mttt) cc_final: 0.8708 (mttm) REVERT: D 116 ASN cc_start: 0.8806 (m110) cc_final: 0.8030 (t0) REVERT: D 121 LYS cc_start: 0.8953 (tptp) cc_final: 0.8712 (tptp) REVERT: F 51 LYS cc_start: 0.9104 (mmtt) cc_final: 0.8841 (ptpt) REVERT: F 54 ARG cc_start: 0.8279 (mtp85) cc_final: 0.8074 (ttm110) REVERT: F 58 LYS cc_start: 0.9014 (mttt) cc_final: 0.8740 (mmtt) REVERT: F 64 HIS cc_start: 0.8293 (m-70) cc_final: 0.7971 (m170) outliers start: 16 outliers final: 10 residues processed: 174 average time/residue: 0.1873 time to fit residues: 38.4701 Evaluate side-chains 155 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 20 optimal weight: 0.0020 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 21 optimal weight: 0.0970 chunk 12 optimal weight: 0.0870 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 0.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 322 ASN B 60 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN E 296 ASN E 311 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN F 106 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.133549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.099892 restraints weight = 6768.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.099773 restraints weight = 5764.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.101789 restraints weight = 4817.969| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3906 Z= 0.138 Angle : 0.770 12.447 5286 Z= 0.410 Chirality : 0.045 0.193 627 Planarity : 0.005 0.047 684 Dihedral : 4.792 35.840 561 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.45 % Allowed : 24.83 % Favored : 71.72 % 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: 0.61 (0.40), residues: 459 helix: 3.28 (0.28), residues: 261 sheet: -3.90 (0.50), residues: 30 loop : -3.82 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 92 HIS 0.010 0.003 HIS B 106 PHE 0.005 0.001 PHE B 70 TYR 0.006 0.001 TYR C 302 ARG 0.006 0.001 ARG B 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 3) link_NAG-ASN : angle 2.43120 ( 9) hydrogen bonds : bond 0.03428 ( 273) hydrogen bonds : angle 3.55876 ( 792) SS BOND : bond 0.00238 ( 3) SS BOND : angle 1.32006 ( 6) covalent geometry : bond 0.00289 ( 3900) covalent geometry : angle 0.76321 ( 5271) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7444 (mmmt) cc_final: 0.7013 (mtpp) REVERT: B 64 HIS cc_start: 0.7949 (m-70) cc_final: 0.7325 (t-90) REVERT: C 290 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8112 (m-40) REVERT: C 307 LYS cc_start: 0.7483 (mmmt) cc_final: 0.7182 (mtpp) REVERT: E 22 ASN cc_start: 0.6971 (m-40) cc_final: 0.6673 (t0) REVERT: E 290 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7869 (m-40) REVERT: E 320 MET cc_start: 0.6711 (ttm) cc_final: 0.6437 (ttm) REVERT: D 51 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8686 (mtmm) REVERT: D 58 LYS cc_start: 0.8890 (mttt) cc_final: 0.8639 (mttm) REVERT: F 64 HIS cc_start: 0.8044 (m-70) cc_final: 0.7448 (t-170) outliers start: 15 outliers final: 8 residues processed: 157 average time/residue: 0.1909 time to fit residues: 35.3402 Evaluate side-chains 150 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 322 ASN E 295 GLN E 296 ASN E 322 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.135672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.103368 restraints weight = 6870.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104378 restraints weight = 5662.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.105419 restraints weight = 4648.453| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3906 Z= 0.170 Angle : 0.846 13.633 5286 Z= 0.443 Chirality : 0.048 0.204 627 Planarity : 0.006 0.049 684 Dihedral : 4.815 36.004 561 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.22 % Allowed : 27.13 % Favored : 69.66 % 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: 0.50 (0.40), residues: 459 helix: 3.11 (0.28), residues: 261 sheet: -3.73 (0.55), residues: 30 loop : -3.78 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 92 HIS 0.009 0.003 HIS B 106 PHE 0.007 0.001 PHE B 70 TYR 0.014 0.002 TYR C 302 ARG 0.007 0.001 ARG B 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 3) link_NAG-ASN : angle 2.66552 ( 9) hydrogen bonds : bond 0.03761 ( 273) hydrogen bonds : angle 3.76888 ( 792) SS BOND : bond 0.00427 ( 3) SS BOND : angle 0.96099 ( 6) covalent geometry : bond 0.00384 ( 3900) covalent geometry : angle 0.83976 ( 5271) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7221 (tm-30) REVERT: A 307 LYS cc_start: 0.7487 (mmmt) cc_final: 0.7015 (mtpp) REVERT: A 320 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6817 (ttp) REVERT: B 58 LYS cc_start: 0.8812 (mmtp) cc_final: 0.8550 (mmtp) REVERT: B 64 HIS cc_start: 0.7883 (m-70) cc_final: 0.7274 (t-90) REVERT: C 290 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.8097 (m-40) REVERT: C 307 LYS cc_start: 0.7538 (mmmt) cc_final: 0.7246 (mtpp) REVERT: E 22 ASN cc_start: 0.7061 (m-40) cc_final: 0.6785 (t0) REVERT: E 290 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.8025 (m-40) REVERT: E 320 MET cc_start: 0.7092 (ttm) cc_final: 0.6726 (ttm) REVERT: D 51 LYS cc_start: 0.9207 (ptpt) cc_final: 0.8968 (ptpp) REVERT: D 58 LYS cc_start: 0.8843 (mttt) cc_final: 0.8615 (mttm) REVERT: F 51 LYS cc_start: 0.8809 (mtmm) cc_final: 0.8567 (mtmm) REVERT: F 54 ARG cc_start: 0.8178 (ttm110) cc_final: 0.7922 (ptp90) REVERT: F 64 HIS cc_start: 0.7871 (m-70) cc_final: 0.7353 (t-170) REVERT: F 114 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8509 (mt-10) outliers start: 14 outliers final: 8 residues processed: 159 average time/residue: 0.1865 time to fit residues: 34.9758 Evaluate side-chains 161 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 0.0870 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 322 ASN E 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.135592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.094900 restraints weight = 6700.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.097537 restraints weight = 4392.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.099263 restraints weight = 3473.684| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3906 Z= 0.172 Angle : 0.847 14.840 5286 Z= 0.443 Chirality : 0.046 0.173 627 Planarity : 0.005 0.048 684 Dihedral : 4.831 36.376 561 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.91 % Allowed : 27.13 % Favored : 68.97 % 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: 0.56 (0.40), residues: 459 helix: 3.08 (0.28), residues: 261 sheet: -3.52 (0.60), residues: 30 loop : -3.61 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 92 HIS 0.011 0.004 HIS D 106 PHE 0.006 0.001 PHE F 70 TYR 0.013 0.002 TYR C 302 ARG 0.008 0.001 ARG B 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 3) link_NAG-ASN : angle 2.76497 ( 9) hydrogen bonds : bond 0.03831 ( 273) hydrogen bonds : angle 3.75170 ( 792) SS BOND : bond 0.00205 ( 3) SS BOND : angle 0.72290 ( 6) covalent geometry : bond 0.00387 ( 3900) covalent geometry : angle 0.84060 ( 5271) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7212 (tm-30) REVERT: A 307 LYS cc_start: 0.7776 (mmmt) cc_final: 0.7281 (mtpp) REVERT: B 121 LYS cc_start: 0.8929 (tmtt) cc_final: 0.8692 (tptp) REVERT: C 290 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8134 (m-40) REVERT: C 307 LYS cc_start: 0.7793 (mmmt) cc_final: 0.7437 (mtpp) REVERT: E 22 ASN cc_start: 0.7007 (m-40) cc_final: 0.6726 (t0) REVERT: E 290 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8127 (m-40) REVERT: E 320 MET cc_start: 0.7014 (ttm) cc_final: 0.6729 (ttm) REVERT: D 51 LYS cc_start: 0.9441 (ptpt) cc_final: 0.9161 (ptpp) REVERT: D 54 ARG cc_start: 0.8657 (ttm110) cc_final: 0.8369 (ttm110) REVERT: D 58 LYS cc_start: 0.9049 (mttt) cc_final: 0.8720 (mttm) REVERT: F 58 LYS cc_start: 0.9107 (mttt) cc_final: 0.8651 (mmtp) REVERT: F 64 HIS cc_start: 0.8053 (m-70) cc_final: 0.7515 (t-170) REVERT: F 67 GLU cc_start: 0.7623 (pp20) cc_final: 0.7377 (pp20) outliers start: 17 outliers final: 10 residues processed: 163 average time/residue: 0.1939 time to fit residues: 37.3526 Evaluate side-chains 160 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 322 ASN E 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.132870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.092105 restraints weight = 6879.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.094790 restraints weight = 4587.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.096361 restraints weight = 3637.021| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3906 Z= 0.229 Angle : 0.886 12.030 5286 Z= 0.476 Chirality : 0.050 0.177 627 Planarity : 0.006 0.041 684 Dihedral : 5.092 36.802 561 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.60 % Allowed : 28.97 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.39), residues: 459 helix: 2.79 (0.28), residues: 261 sheet: -3.64 (0.58), residues: 36 loop : -3.38 (0.42), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 92 HIS 0.012 0.004 HIS D 106 PHE 0.008 0.001 PHE F 70 TYR 0.017 0.003 TYR C 302 ARG 0.008 0.001 ARG B 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 3) link_NAG-ASN : angle 3.80816 ( 9) hydrogen bonds : bond 0.04139 ( 273) hydrogen bonds : angle 4.08237 ( 792) SS BOND : bond 0.00397 ( 3) SS BOND : angle 0.41494 ( 6) covalent geometry : bond 0.00524 ( 3900) covalent geometry : angle 0.87353 ( 5271) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7874 (mmmt) cc_final: 0.7377 (mtpp) REVERT: B 58 LYS cc_start: 0.9150 (mmtp) cc_final: 0.8734 (mmtp) REVERT: B 64 HIS cc_start: 0.8120 (m-70) cc_final: 0.7459 (t-170) REVERT: B 121 LYS cc_start: 0.8929 (tmtt) cc_final: 0.8709 (tptp) REVERT: C 307 LYS cc_start: 0.7695 (mmmt) cc_final: 0.7311 (mtpp) REVERT: C 315 LYS cc_start: 0.8099 (mmtm) cc_final: 0.7816 (mmtm) REVERT: E 22 ASN cc_start: 0.7134 (m-40) cc_final: 0.6846 (t0) REVERT: E 302 TYR cc_start: 0.4133 (t80) cc_final: 0.2602 (m-80) REVERT: D 54 ARG cc_start: 0.8725 (ttm110) cc_final: 0.8423 (ttm110) REVERT: D 58 LYS cc_start: 0.9090 (mttt) cc_final: 0.8774 (mttm) REVERT: D 64 HIS cc_start: 0.8146 (OUTLIER) cc_final: 0.7436 (t-90) REVERT: F 37 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.7837 (t70) REVERT: F 58 LYS cc_start: 0.9151 (mttt) cc_final: 0.8757 (mttm) REVERT: F 64 HIS cc_start: 0.8114 (m-70) cc_final: 0.7479 (t-170) outliers start: 20 outliers final: 11 residues processed: 165 average time/residue: 0.1908 time to fit residues: 37.0293 Evaluate side-chains 161 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 43 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 ASN C 322 ASN E 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.133958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.093746 restraints weight = 6791.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.096356 restraints weight = 4561.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.098032 restraints weight = 3627.110| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 3906 Z= 0.195 Angle : 0.940 13.207 5286 Z= 0.500 Chirality : 0.052 0.311 627 Planarity : 0.006 0.041 684 Dihedral : 5.100 36.475 561 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.60 % Allowed : 30.11 % Favored : 65.29 % 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: 0.37 (0.39), residues: 459 helix: 2.64 (0.28), residues: 261 sheet: -3.49 (0.62), residues: 36 loop : -3.13 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 92 HIS 0.012 0.004 HIS B 106 PHE 0.006 0.001 PHE B 70 TYR 0.012 0.003 TYR C 302 ARG 0.010 0.001 ARG B 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 3) link_NAG-ASN : angle 4.17105 ( 9) hydrogen bonds : bond 0.04350 ( 273) hydrogen bonds : angle 4.10278 ( 792) SS BOND : bond 0.00047 ( 3) SS BOND : angle 0.30125 ( 6) covalent geometry : bond 0.00439 ( 3900) covalent geometry : angle 0.92539 ( 5271) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 307 LYS cc_start: 0.7936 (mmmt) cc_final: 0.7420 (mtpp) REVERT: B 58 LYS cc_start: 0.9114 (mmtp) cc_final: 0.8667 (mmtp) REVERT: C 307 LYS cc_start: 0.7767 (mmmt) cc_final: 0.7360 (mtpp) REVERT: E 22 ASN cc_start: 0.7080 (m-40) cc_final: 0.6861 (t0) REVERT: E 290 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8077 (m-40) REVERT: E 302 TYR cc_start: 0.4180 (t80) cc_final: 0.2746 (m-80) REVERT: D 51 LYS cc_start: 0.9437 (ptpt) cc_final: 0.9184 (ptpp) REVERT: D 54 ARG cc_start: 0.8661 (ttm110) cc_final: 0.8382 (ttm110) REVERT: D 58 LYS cc_start: 0.9061 (mttt) cc_final: 0.8750 (mttm) REVERT: D 64 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7412 (t-90) REVERT: F 37 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.7750 (t70) REVERT: F 54 ARG cc_start: 0.8701 (ttm110) cc_final: 0.8321 (ptp-110) REVERT: F 64 HIS cc_start: 0.8048 (m-70) cc_final: 0.7578 (t-170) outliers start: 20 outliers final: 11 residues processed: 162 average time/residue: 0.1840 time to fit residues: 35.2059 Evaluate side-chains 164 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 16 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 0.0370 chunk 41 optimal weight: 0.9980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 322 ASN E 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.134880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.094740 restraints weight = 6672.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.097380 restraints weight = 4478.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.098952 restraints weight = 3567.444| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3906 Z= 0.189 Angle : 1.032 15.979 5286 Z= 0.535 Chirality : 0.052 0.271 627 Planarity : 0.006 0.040 684 Dihedral : 5.103 36.458 561 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.83 % Allowed : 30.57 % Favored : 64.60 % 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: 0.28 (0.40), residues: 459 helix: 2.49 (0.29), residues: 261 sheet: -3.46 (0.62), residues: 36 loop : -3.02 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 92 HIS 0.016 0.004 HIS B 106 PHE 0.005 0.001 PHE B 70 TYR 0.010 0.002 TYR C 302 ARG 0.011 0.001 ARG B 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 3) link_NAG-ASN : angle 4.09587 ( 9) hydrogen bonds : bond 0.04441 ( 273) hydrogen bonds : angle 4.28151 ( 792) SS BOND : bond 0.00103 ( 3) SS BOND : angle 0.28896 ( 6) covalent geometry : bond 0.00415 ( 3900) covalent geometry : angle 1.01902 ( 5271) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7443 (mtpp) REVERT: C 307 LYS cc_start: 0.7729 (mmmt) cc_final: 0.7301 (mtpp) REVERT: E 315 LYS cc_start: 0.8246 (mmtm) cc_final: 0.7886 (tppt) REVERT: D 51 LYS cc_start: 0.9454 (ptpt) cc_final: 0.9089 (ptpp) REVERT: D 54 ARG cc_start: 0.8659 (ttm110) cc_final: 0.8370 (ttm110) REVERT: D 58 LYS cc_start: 0.9058 (mttt) cc_final: 0.8750 (mttm) REVERT: D 64 HIS cc_start: 0.8050 (OUTLIER) cc_final: 0.7428 (t-90) REVERT: D 121 LYS cc_start: 0.8951 (tptp) cc_final: 0.8633 (tptp) REVERT: F 37 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.7755 (t70) REVERT: F 54 ARG cc_start: 0.8692 (ttm110) cc_final: 0.8354 (ptp-110) REVERT: F 64 HIS cc_start: 0.8032 (m-70) cc_final: 0.7597 (t-170) outliers start: 21 outliers final: 11 residues processed: 163 average time/residue: 0.1853 time to fit residues: 35.6123 Evaluate side-chains 162 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN C 296 ASN C 312 ASN C 322 ASN E 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.132652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.092627 restraints weight = 6846.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.095144 restraints weight = 4640.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.096498 restraints weight = 3709.164| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3906 Z= 0.259 Angle : 1.057 16.201 5286 Z= 0.557 Chirality : 0.054 0.199 627 Planarity : 0.006 0.042 684 Dihedral : 5.509 37.156 561 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 4.83 % Allowed : 31.49 % Favored : 63.68 % 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: 0.04 (0.39), residues: 459 helix: 2.24 (0.29), residues: 261 sheet: -3.45 (0.64), residues: 36 loop : -3.07 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 92 HIS 0.016 0.005 HIS B 106 PHE 0.007 0.001 PHE F 70 TYR 0.016 0.003 TYR C 302 ARG 0.011 0.001 ARG B 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 3) link_NAG-ASN : angle 4.73763 ( 9) hydrogen bonds : bond 0.04783 ( 273) hydrogen bonds : angle 4.47768 ( 792) SS BOND : bond 0.00151 ( 3) SS BOND : angle 1.65926 ( 6) covalent geometry : bond 0.00588 ( 3900) covalent geometry : angle 1.03856 ( 5271) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7681 (mtpp) REVERT: C 307 LYS cc_start: 0.7747 (mmmt) cc_final: 0.7324 (mtpp) REVERT: E 315 LYS cc_start: 0.8301 (mmtm) cc_final: 0.7959 (tppt) REVERT: D 54 ARG cc_start: 0.8754 (ttm110) cc_final: 0.8449 (ttm110) REVERT: D 58 LYS cc_start: 0.9072 (mttt) cc_final: 0.8761 (mttm) REVERT: D 64 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7611 (t-90) REVERT: D 121 LYS cc_start: 0.8917 (tptp) cc_final: 0.8628 (tptp) REVERT: F 37 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.7710 (t70) REVERT: F 54 ARG cc_start: 0.8727 (ttm110) cc_final: 0.8369 (ptp-110) REVERT: F 64 HIS cc_start: 0.8111 (m-70) cc_final: 0.7717 (t-170) REVERT: F 120 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8616 (mm-30) REVERT: F 121 LYS cc_start: 0.8621 (tptp) cc_final: 0.8418 (tptp) outliers start: 21 outliers final: 11 residues processed: 160 average time/residue: 0.1910 time to fit residues: 36.1189 Evaluate side-chains 163 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 chunk 44 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 322 ASN E 296 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.133493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.093388 restraints weight = 6685.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.096033 restraints weight = 4461.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.097657 restraints weight = 3546.546| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 3906 Z= 0.213 Angle : 1.104 16.573 5286 Z= 0.575 Chirality : 0.053 0.200 627 Planarity : 0.006 0.044 684 Dihedral : 5.565 37.199 561 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.68 % Allowed : 32.87 % Favored : 63.45 % 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: 0.07 (0.39), residues: 459 helix: 2.20 (0.29), residues: 261 sheet: -3.35 (0.65), residues: 36 loop : -2.96 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 92 HIS 0.015 0.004 HIS B 106 PHE 0.006 0.001 PHE F 70 TYR 0.011 0.002 TYR C 302 ARG 0.011 0.001 ARG B 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00837 ( 3) link_NAG-ASN : angle 5.05479 ( 9) hydrogen bonds : bond 0.04682 ( 273) hydrogen bonds : angle 4.46068 ( 792) SS BOND : bond 0.00070 ( 3) SS BOND : angle 1.18934 ( 6) covalent geometry : bond 0.00471 ( 3900) covalent geometry : angle 1.08509 ( 5271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2534.78 seconds wall clock time: 45 minutes 30.15 seconds (2730.15 seconds total)