Starting phenix.real_space_refine on Fri Jun 6 07:42:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5j_37294/06_2025/8w5j_37294.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5j_37294/06_2025/8w5j_37294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w5j_37294/06_2025/8w5j_37294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5j_37294/06_2025/8w5j_37294.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5j_37294/06_2025/8w5j_37294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5j_37294/06_2025/8w5j_37294.cif" } resolution = 4.4 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= 0.002 sd= 0.023 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 P 1 5.49 5 S 22 5.16 5 C 4718 2.51 5 N 1225 2.21 5 O 1390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7356 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2369 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "C" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "E" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 4, 'TRANS': 37} Chain: "I" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2369 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "K" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "M" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 4, 'TRANS': 37} Chain: "I" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'46E': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Time building chain proxies: 4.78, per 1000 atoms: 0.65 Number of scatterers: 7356 At special positions: 0 Unit cell: (94.16, 104.86, 138.03, 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) S 22 16.00 P 1 15.00 O 1390 8.00 N 1225 7.00 C 4718 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 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 894.2 milliseconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 2 sheets defined 37.2% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 49 through 55 removed outlier: 3.671A pdb=" N GLN A 53 " --> pdb=" O HIS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'B' and resid 87 through 135 Proline residue: B 112 - end of helix Processing helix chain 'C' and resid 14 through 49 Proline residue: C 39 - end of helix Processing helix chain 'D' and resid 30 through 51 Processing helix chain 'D' and resid 52 through 58 Processing helix chain 'E' and resid 20 through 44 removed outlier: 3.809A pdb=" N ASN E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL E 27 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS E 29 " --> pdb=" O HIS E 25 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE E 33 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Proline residue: E 34 - end of helix Processing helix chain 'E' and resid 49 through 55 Processing helix chain 'I' and resid 50 through 56 removed outlier: 3.953A pdb=" N GLU I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 66 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 364 through 373 removed outlier: 3.575A pdb=" N GLN I 372 " --> pdb=" O LEU I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 135 Proline residue: J 112 - end of helix Processing helix chain 'K' and resid 14 through 49 Proline residue: K 39 - end of helix Processing helix chain 'L' and resid 30 through 51 Processing helix chain 'L' and resid 51 through 58 removed outlier: 4.019A pdb=" N ASP L 55 " --> pdb=" O SER L 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 31 removed outlier: 3.558A pdb=" N ALA M 28 " --> pdb=" O THR M 24 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS M 29 " --> pdb=" O HIS M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 44 Processing helix chain 'M' and resid 49 through 55 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 93 removed outlier: 6.930A pdb=" N PHE A 98 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 269 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 263 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 302 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 313 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 317 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 357 " --> pdb=" O ARG A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 84 through 93 removed outlier: 7.274A pdb=" N PHE I 98 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET I 164 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL I 196 " --> pdb=" O LEU I 183 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU I 209 " --> pdb=" O VAL I 205 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU I 255 " --> pdb=" O LEU I 275 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU I 268 " --> pdb=" O LYS I 306 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I 337 " --> pdb=" O GLN I 358 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG I 85 " --> pdb=" O LEU I 357 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N PHE I 359 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP I 87 " --> pdb=" O PHE I 359 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N THR I 361 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASN I 89 " --> pdb=" O THR I 361 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1500 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: 2.10 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1306 1.33 - 1.45: 1978 1.45 - 1.57: 4192 1.57 - 1.69: 3 1.69 - 1.81: 36 Bond restraints: 7515 Sorted by residual: bond pdb=" CA ASP A 134 " pdb=" CB ASP A 134 " ideal model delta sigma weight residual 1.532 1.548 -0.016 1.33e-02 5.65e+03 1.40e+00 bond pdb=" CB ASP I 134 " pdb=" CG ASP I 134 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.22e+00 bond pdb=" CA VAL E 60 " pdb=" CB VAL E 60 " ideal model delta sigma weight residual 1.540 1.569 -0.029 2.70e-02 1.37e+03 1.17e+00 bond pdb=" CA VAL M 60 " pdb=" CB VAL M 60 " ideal model delta sigma weight residual 1.540 1.568 -0.028 2.70e-02 1.37e+03 1.08e+00 bond pdb=" CB ASP A 134 " pdb=" CG ASP A 134 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.01e+00 ... (remaining 7510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 9929 1.59 - 3.19: 205 3.19 - 4.78: 40 4.78 - 6.38: 12 6.38 - 7.97: 10 Bond angle restraints: 10196 Sorted by residual: angle pdb=" CA PRO I 185 " pdb=" N PRO I 185 " pdb=" CD PRO I 185 " ideal model delta sigma weight residual 112.00 107.38 4.62 1.40e+00 5.10e-01 1.09e+01 angle pdb=" C ASN A 133 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " ideal model delta sigma weight residual 124.82 130.42 -5.60 1.78e+00 3.16e-01 9.90e+00 angle pdb=" C ASN I 133 " pdb=" N ASP I 134 " pdb=" CA ASP I 134 " ideal model delta sigma weight residual 125.66 130.23 -4.57 1.85e+00 2.92e-01 6.11e+00 angle pdb=" CA LEU D 57 " pdb=" CB LEU D 57 " pdb=" CG LEU D 57 " ideal model delta sigma weight residual 116.30 124.27 -7.97 3.50e+00 8.16e-02 5.19e+00 angle pdb=" C SER E 59 " pdb=" N VAL E 60 " pdb=" CA VAL E 60 " ideal model delta sigma weight residual 121.70 125.78 -4.08 1.80e+00 3.09e-01 5.13e+00 ... (remaining 10191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 4069 17.28 - 34.56: 307 34.56 - 51.84: 43 51.84 - 69.12: 11 69.12 - 86.40: 2 Dihedral angle restraints: 4432 sinusoidal: 1714 harmonic: 2718 Sorted by residual: dihedral pdb=" CA ASN A 95 " pdb=" C ASN A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual 180.00 151.93 28.07 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA ASN I 95 " pdb=" C ASN I 95 " pdb=" N PRO I 96 " pdb=" CA PRO I 96 " ideal model delta harmonic sigma weight residual 180.00 155.14 24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ASN A 133 " pdb=" C ASN A 133 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " ideal model delta harmonic sigma weight residual -180.00 -159.25 -20.75 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 4429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 701 0.029 - 0.058: 314 0.058 - 0.087: 85 0.087 - 0.116: 50 0.116 - 0.145: 7 Chirality restraints: 1157 Sorted by residual: chirality pdb=" CA ILE I 353 " pdb=" N ILE I 353 " pdb=" C ILE I 353 " pdb=" CB ILE I 353 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE I 344 " pdb=" N ILE I 344 " pdb=" C ILE I 344 " pdb=" CB ILE I 344 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE A 303 " pdb=" N ILE A 303 " pdb=" C ILE A 303 " pdb=" CB ILE A 303 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1154 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I 184 " -0.073 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO I 185 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO I 185 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO I 185 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 206 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 207 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 33 " 0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO E 34 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 34 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 34 " 0.023 5.00e-02 4.00e+02 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 302 2.72 - 3.26: 7779 3.26 - 3.81: 12230 3.81 - 4.35: 13958 4.35 - 4.90: 24143 Nonbonded interactions: 58412 Sorted by model distance: nonbonded pdb=" OG SER I 218 " pdb=" OD1 ASP I 227 " model vdw 2.174 3.040 nonbonded pdb=" OD1 ASN A 179 " pdb=" OG SER A 200 " model vdw 2.191 3.040 nonbonded pdb=" OG SER I 151 " pdb=" OE1 GLN I 169 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASN I 179 " pdb=" OG SER I 200 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR A 62 " pdb=" OD1 ASN A 65 " model vdw 2.231 3.040 ... (remaining 58407 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' selection = (chain 'I' and resid 49 through 373) } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } 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 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: 2.530 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.600 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.002 0.036 7515 Z= 0.118 Angle : 0.631 7.970 10196 Z= 0.310 Chirality : 0.039 0.145 1157 Planarity : 0.005 0.109 1298 Dihedral : 12.495 86.405 2672 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 1.07 (0.29), residues: 918 helix: 2.12 (0.28), residues: 324 sheet: 0.18 (0.27), residues: 378 loop : -0.30 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 42 HIS 0.004 0.001 HIS A 346 PHE 0.016 0.001 PHE I 340 TYR 0.018 0.001 TYR I 314 ARG 0.004 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.21990 ( 518) hydrogen bonds : angle 8.02147 ( 1500) covalent geometry : bond 0.00237 ( 7515) covalent geometry : angle 0.63060 (10196) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: D 54 MET cc_start: 0.8156 (ptt) cc_final: 0.7902 (ptt) REVERT: I 352 LYS cc_start: 0.9468 (mttp) cc_final: 0.9231 (mmtm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1344 time to fit residues: 15.3820 Evaluate side-chains 56 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.044650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.036595 restraints weight = 74354.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.037611 restraints weight = 46076.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.038340 restraints weight = 32449.136| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7515 Z= 0.186 Angle : 0.647 8.847 10196 Z= 0.341 Chirality : 0.042 0.201 1157 Planarity : 0.005 0.073 1298 Dihedral : 6.947 77.302 1000 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.13 % Allowed : 4.79 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.08 (0.29), residues: 918 helix: 2.09 (0.28), residues: 328 sheet: 0.04 (0.25), residues: 400 loop : 0.09 (0.55), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 260 HIS 0.007 0.001 HIS A 346 PHE 0.013 0.001 PHE I 116 TYR 0.016 0.002 TYR I 143 ARG 0.003 0.000 ARG I 219 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 518) hydrogen bonds : angle 5.95970 ( 1500) covalent geometry : bond 0.00382 ( 7515) covalent geometry : angle 0.64750 (10196) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.1206 time to fit residues: 13.7890 Evaluate side-chains 52 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 17 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN I 133 ASN I 248 GLN M 25 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.044646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.036525 restraints weight = 74445.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.037530 restraints weight = 46211.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.038255 restraints weight = 32654.310| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7515 Z= 0.147 Angle : 0.616 8.911 10196 Z= 0.313 Chirality : 0.041 0.177 1157 Planarity : 0.005 0.058 1298 Dihedral : 6.778 75.349 1000 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.13 % Allowed : 4.66 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.00 (0.29), residues: 918 helix: 2.11 (0.27), residues: 328 sheet: 0.04 (0.26), residues: 370 loop : -0.23 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 260 HIS 0.005 0.001 HIS A 346 PHE 0.013 0.001 PHE A 176 TYR 0.014 0.002 TYR I 314 ARG 0.001 0.000 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 518) hydrogen bonds : angle 5.58143 ( 1500) covalent geometry : bond 0.00304 ( 7515) covalent geometry : angle 0.61619 (10196) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8717 (m-80) cc_final: 0.8290 (m-10) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.1271 time to fit residues: 14.2253 Evaluate side-chains 52 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN I 266 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.045281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.037241 restraints weight = 72242.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.038280 restraints weight = 43896.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.039023 restraints weight = 30772.711| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7515 Z= 0.109 Angle : 0.613 7.145 10196 Z= 0.304 Chirality : 0.042 0.177 1157 Planarity : 0.004 0.054 1298 Dihedral : 6.608 73.077 1000 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.12 (0.29), residues: 918 helix: 2.25 (0.28), residues: 328 sheet: -0.07 (0.25), residues: 400 loop : 0.16 (0.56), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 42 HIS 0.003 0.001 HIS A 346 PHE 0.013 0.001 PHE A 359 TYR 0.011 0.001 TYR D 33 ARG 0.001 0.000 ARG I 310 Details of bonding type rmsd hydrogen bonds : bond 0.02879 ( 518) hydrogen bonds : angle 5.24167 ( 1500) covalent geometry : bond 0.00225 ( 7515) covalent geometry : angle 0.61276 (10196) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8645 (m-80) cc_final: 0.8260 (m-10) REVERT: A 303 ILE cc_start: 0.9352 (pt) cc_final: 0.9092 (pt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1356 time to fit residues: 16.0503 Evaluate side-chains 55 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 84 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 43 optimal weight: 0.0570 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.044516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.036322 restraints weight = 73112.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.037379 restraints weight = 44413.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.038110 restraints weight = 31119.651| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7515 Z= 0.138 Angle : 0.602 8.322 10196 Z= 0.304 Chirality : 0.041 0.170 1157 Planarity : 0.004 0.053 1298 Dihedral : 6.565 72.776 1000 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.07 (0.29), residues: 918 helix: 2.24 (0.28), residues: 328 sheet: -0.08 (0.25), residues: 406 loop : 0.06 (0.57), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 42 HIS 0.004 0.001 HIS A 346 PHE 0.011 0.001 PHE A 359 TYR 0.013 0.001 TYR D 33 ARG 0.003 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02929 ( 518) hydrogen bonds : angle 5.16271 ( 1500) covalent geometry : bond 0.00289 ( 7515) covalent geometry : angle 0.60234 (10196) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8763 (m-80) cc_final: 0.8395 (m-10) REVERT: I 259 LEU cc_start: 0.9270 (tp) cc_final: 0.9051 (tp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1398 time to fit residues: 14.7431 Evaluate side-chains 55 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 3 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 371 GLN ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.042962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.035017 restraints weight = 75846.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.036015 restraints weight = 45624.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.036712 restraints weight = 31931.096| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7515 Z= 0.262 Angle : 0.699 14.468 10196 Z= 0.359 Chirality : 0.042 0.165 1157 Planarity : 0.005 0.055 1298 Dihedral : 7.038 70.923 1000 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.60 (0.28), residues: 918 helix: 1.82 (0.27), residues: 328 sheet: -0.24 (0.25), residues: 404 loop : -0.37 (0.53), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 243 HIS 0.007 0.002 HIS A 346 PHE 0.024 0.002 PHE A 359 TYR 0.015 0.002 TYR I 143 ARG 0.004 0.001 ARG I 140 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 518) hydrogen bonds : angle 5.43569 ( 1500) covalent geometry : bond 0.00531 ( 7515) covalent geometry : angle 0.69853 (10196) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8869 (m-80) cc_final: 0.8559 (m-10) REVERT: A 307 TYR cc_start: 0.9166 (m-80) cc_final: 0.8607 (m-80) REVERT: C 40 MET cc_start: 0.9596 (mpp) cc_final: 0.9368 (mpp) REVERT: I 259 LEU cc_start: 0.9327 (tp) cc_final: 0.9107 (tp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1279 time to fit residues: 13.1105 Evaluate side-chains 48 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.1980 chunk 74 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.044016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.035886 restraints weight = 73942.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.036936 restraints weight = 44490.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.037620 restraints weight = 30879.064| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7515 Z= 0.131 Angle : 0.632 9.923 10196 Z= 0.314 Chirality : 0.042 0.165 1157 Planarity : 0.005 0.076 1298 Dihedral : 6.759 69.300 1000 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.78 (0.29), residues: 918 helix: 2.06 (0.27), residues: 328 sheet: -0.28 (0.25), residues: 402 loop : -0.10 (0.54), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 42 HIS 0.004 0.001 HIS A 346 PHE 0.026 0.001 PHE D 42 TYR 0.016 0.001 TYR D 33 ARG 0.002 0.000 ARG I 315 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 518) hydrogen bonds : angle 5.21253 ( 1500) covalent geometry : bond 0.00274 ( 7515) covalent geometry : angle 0.63235 (10196) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8865 (m-80) cc_final: 0.8602 (m-10) REVERT: I 259 LEU cc_start: 0.9359 (tp) cc_final: 0.9151 (tp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1233 time to fit residues: 14.3430 Evaluate side-chains 51 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.042941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.034972 restraints weight = 77364.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.035978 restraints weight = 45842.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.036705 restraints weight = 31767.510| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7515 Z= 0.221 Angle : 0.660 13.102 10196 Z= 0.337 Chirality : 0.041 0.148 1157 Planarity : 0.005 0.064 1298 Dihedral : 6.971 68.085 1000 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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 (0.29), residues: 918 helix: 1.89 (0.27), residues: 330 sheet: -0.31 (0.25), residues: 406 loop : -0.33 (0.54), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 243 HIS 0.006 0.001 HIS A 346 PHE 0.029 0.002 PHE D 42 TYR 0.013 0.002 TYR I 114 ARG 0.003 0.000 ARG I 219 Details of bonding type rmsd hydrogen bonds : bond 0.03171 ( 518) hydrogen bonds : angle 5.30136 ( 1500) covalent geometry : bond 0.00451 ( 7515) covalent geometry : angle 0.66037 (10196) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8868 (m-80) cc_final: 0.8262 (m-80) REVERT: I 259 LEU cc_start: 0.9320 (tp) cc_final: 0.9086 (tp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1475 time to fit residues: 14.5608 Evaluate side-chains 50 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN I 133 ASN I 248 GLN I 321 ASN K 43 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.042994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.035024 restraints weight = 77245.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.036037 restraints weight = 45755.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.036744 restraints weight = 31663.184| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7515 Z= 0.187 Angle : 0.657 11.674 10196 Z= 0.334 Chirality : 0.042 0.196 1157 Planarity : 0.005 0.061 1298 Dihedral : 6.916 67.951 1000 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.13 % Allowed : 1.26 % Favored : 98.61 % 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: 0.55 (0.29), residues: 918 helix: 1.92 (0.27), residues: 330 sheet: -0.43 (0.25), residues: 402 loop : -0.26 (0.54), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 42 HIS 0.006 0.001 HIS A 346 PHE 0.031 0.002 PHE D 42 TYR 0.012 0.002 TYR I 114 ARG 0.005 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 518) hydrogen bonds : angle 5.28234 ( 1500) covalent geometry : bond 0.00384 ( 7515) covalent geometry : angle 0.65698 (10196) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8843 (m-80) cc_final: 0.8244 (m-80) REVERT: A 307 TYR cc_start: 0.9203 (m-80) cc_final: 0.8558 (m-80) REVERT: B 126 MET cc_start: 0.9681 (ppp) cc_final: 0.9439 (ppp) REVERT: I 259 LEU cc_start: 0.9320 (tp) cc_final: 0.9093 (tp) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.1314 time to fit residues: 13.6328 Evaluate side-chains 49 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 28 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN I 133 ASN I 169 GLN I 248 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.043613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.035664 restraints weight = 73992.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.036680 restraints weight = 44120.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.037396 restraints weight = 30595.461| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7515 Z= 0.122 Angle : 0.647 9.449 10196 Z= 0.318 Chirality : 0.042 0.169 1157 Planarity : 0.005 0.058 1298 Dihedral : 6.734 69.108 1000 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.13 % Allowed : 0.38 % Favored : 99.50 % 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: 0.74 (0.29), residues: 918 helix: 2.08 (0.27), residues: 329 sheet: -0.32 (0.25), residues: 400 loop : -0.20 (0.55), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 42 HIS 0.004 0.001 HIS A 346 PHE 0.029 0.001 PHE D 42 TYR 0.021 0.001 TYR A 314 ARG 0.003 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.02902 ( 518) hydrogen bonds : angle 5.09941 ( 1500) covalent geometry : bond 0.00256 ( 7515) covalent geometry : angle 0.64711 (10196) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8745 (m-80) cc_final: 0.8356 (m-80) REVERT: A 307 TYR cc_start: 0.9217 (m-80) cc_final: 0.8507 (m-80) REVERT: I 259 LEU cc_start: 0.9230 (tp) cc_final: 0.8996 (tp) REVERT: K 40 MET cc_start: 0.9061 (mpp) cc_final: 0.8843 (mpp) REVERT: L 61 LEU cc_start: 0.8785 (pt) cc_final: 0.8396 (mm) outliers start: 1 outliers final: 1 residues processed: 71 average time/residue: 0.1342 time to fit residues: 14.9973 Evaluate side-chains 54 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 0.0060 chunk 17 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 43 optimal weight: 0.0770 chunk 7 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 overall best weight: 2.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN I 133 ASN I 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.042914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.035028 restraints weight = 74865.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.036025 restraints weight = 45102.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.036703 restraints weight = 31367.832| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7515 Z= 0.180 Angle : 0.655 11.815 10196 Z= 0.330 Chirality : 0.042 0.164 1157 Planarity : 0.005 0.059 1298 Dihedral : 6.810 69.501 1000 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.13 % Allowed : 0.88 % Favored : 98.99 % 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: 0.66 (0.29), residues: 918 helix: 2.00 (0.27), residues: 330 sheet: -0.34 (0.25), residues: 406 loop : -0.26 (0.55), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 42 HIS 0.006 0.001 HIS A 346 PHE 0.026 0.002 PHE D 42 TYR 0.016 0.002 TYR A 314 ARG 0.003 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.03021 ( 518) hydrogen bonds : angle 5.15797 ( 1500) covalent geometry : bond 0.00371 ( 7515) covalent geometry : angle 0.65494 (10196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2168.32 seconds wall clock time: 38 minutes 44.46 seconds (2324.46 seconds total)