Starting phenix.real_space_refine on Wed Sep 17 05:16:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9il4_60664/09_2025/9il4_60664.cif Found real_map, /net/cci-nas-00/data/ceres_data/9il4_60664/09_2025/9il4_60664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9il4_60664/09_2025/9il4_60664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9il4_60664/09_2025/9il4_60664.map" model { file = "/net/cci-nas-00/data/ceres_data/9il4_60664/09_2025/9il4_60664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9il4_60664/09_2025/9il4_60664.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.076 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 Fe 2 7.16 5 S 31 5.16 5 C 3238 2.51 5 N 830 2.21 5 O 821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4922 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2454 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2466 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.42, per 1000 atoms: 0.29 Number of scatterers: 4922 At special positions: 0 Unit cell: (93.095, 85.5175, 68.1975, 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) Fe 2 26.01 S 31 16.00 O 821 8.00 N 830 7.00 C 3238 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: 0.49 Conformation dependent library (CDL) restraints added in 140.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 78.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'B' and resid 98 through 118 Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 128 through 148 Proline residue: B 140 - end of helix Processing helix chain 'B' and resid 152 through 180 removed outlier: 3.815A pdb=" N ALA B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 192 Processing helix chain 'B' and resid 194 through 211 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 240 through 257 Processing helix chain 'B' and resid 304 through 321 removed outlier: 3.557A pdb=" N ILE B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 336 through 351 Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 363 through 374 Processing helix chain 'B' and resid 394 through 420 removed outlier: 3.725A pdb=" N ILE B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER B 417 " --> pdb=" O THR B 413 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 439 removed outlier: 3.734A pdb=" N GLY B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 Processing helix chain 'B' and resid 454 through 473 removed outlier: 3.557A pdb=" N LEU B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET B 473 " --> pdb=" O ILE B 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 118 removed outlier: 3.881A pdb=" N GLU A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 125 removed outlier: 3.527A pdb=" N ASP A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 148 removed outlier: 3.762A pdb=" N GLY A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 155 through 180 removed outlier: 3.507A pdb=" N GLY A 167 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 193 Processing helix chain 'A' and resid 194 through 211 removed outlier: 3.782A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 4.163A pdb=" N TYR A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 240 through 257 Processing helix chain 'A' and resid 304 through 321 Processing helix chain 'A' and resid 322 through 325 Processing helix chain 'A' and resid 328 through 332 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 336 through 351 Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 394 through 408 removed outlier: 3.597A pdb=" N LEU A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 420 removed outlier: 3.800A pdb=" N THR A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 439 removed outlier: 3.804A pdb=" N MET A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 removed outlier: 4.126A pdb=" N CYS A 443 " --> pdb=" O GLY A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.689A pdb=" N MET A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 471 removed outlier: 3.527A pdb=" N LEU A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 984 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: 0.70 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1546 1.34 - 1.46: 1125 1.46 - 1.58: 2305 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 5020 Sorted by residual: bond pdb=" C TRP B 232 " pdb=" N PRO B 233 " ideal model delta sigma weight residual 1.334 1.381 -0.048 2.34e-02 1.83e+03 4.14e+00 bond pdb=" C TRP A 232 " pdb=" N PRO A 233 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.64e+00 bond pdb=" C CYS B 443 " pdb=" N PRO B 444 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 5.79e-01 bond pdb=" CB THR A 347 " pdb=" CG2 THR A 347 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 5.04e-01 bond pdb=" CB PRO B 233 " pdb=" CG PRO B 233 " ideal model delta sigma weight residual 1.492 1.457 0.035 5.00e-02 4.00e+02 4.83e-01 ... (remaining 5015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 6713 1.92 - 3.85: 79 3.85 - 5.77: 22 5.77 - 7.69: 5 7.69 - 9.62: 1 Bond angle restraints: 6820 Sorted by residual: angle pdb=" N GLY A 153 " pdb=" CA GLY A 153 " pdb=" C GLY A 153 " ideal model delta sigma weight residual 115.66 110.44 5.22 1.56e+00 4.11e-01 1.12e+01 angle pdb=" N GLY B 440 " pdb=" CA GLY B 440 " pdb=" C GLY B 440 " ideal model delta sigma weight residual 115.66 110.99 4.67 1.63e+00 3.76e-01 8.20e+00 angle pdb=" CA LEU A 350 " pdb=" CB LEU A 350 " pdb=" CG LEU A 350 " ideal model delta sigma weight residual 116.30 125.92 -9.62 3.50e+00 8.16e-02 7.55e+00 angle pdb=" CA TRP B 386 " pdb=" CB TRP B 386 " pdb=" CG TRP B 386 " ideal model delta sigma weight residual 113.60 117.93 -4.33 1.90e+00 2.77e-01 5.20e+00 angle pdb=" CA TRP A 386 " pdb=" CB TRP A 386 " pdb=" CG TRP A 386 " ideal model delta sigma weight residual 113.60 117.89 -4.29 1.90e+00 2.77e-01 5.09e+00 ... (remaining 6815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 2454 17.80 - 35.60: 307 35.60 - 53.40: 90 53.40 - 71.19: 14 71.19 - 88.99: 5 Dihedral angle restraints: 2870 sinusoidal: 1030 harmonic: 1840 Sorted by residual: dihedral pdb=" CA LEU A 157 " pdb=" C LEU A 157 " pdb=" N ARG A 158 " pdb=" CA ARG A 158 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA TRP B 232 " pdb=" C TRP B 232 " pdb=" N PRO B 233 " pdb=" CA PRO B 233 " ideal model delta harmonic sigma weight residual -180.00 -163.54 -16.46 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU A 193 " pdb=" CG GLU A 193 " pdb=" CD GLU A 193 " pdb=" OE1 GLU A 193 " ideal model delta sinusoidal sigma weight residual 0.00 88.99 -88.99 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 2867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 516 0.030 - 0.059: 205 0.059 - 0.088: 77 0.088 - 0.118: 23 0.118 - 0.147: 4 Chirality restraints: 825 Sorted by residual: chirality pdb=" CA PRO B 233 " pdb=" N PRO B 233 " pdb=" C PRO B 233 " pdb=" CB PRO B 233 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ASN A 390 " pdb=" N ASN A 390 " pdb=" C ASN A 390 " pdb=" CB ASN A 390 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA TRP A 232 " pdb=" N TRP A 232 " pdb=" C TRP A 232 " pdb=" CB TRP A 232 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.57e-01 ... (remaining 822 not shown) Planarity restraints: 837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 424 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.86e+00 pdb=" C VAL A 424 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL A 424 " 0.009 2.00e-02 2.50e+03 pdb=" N ARG A 425 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 333 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO B 334 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 334 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 334 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 386 " 0.006 2.00e-02 2.50e+03 1.20e-02 1.43e+00 pdb=" C TRP A 386 " -0.021 2.00e-02 2.50e+03 pdb=" O TRP A 386 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP A 387 " 0.007 2.00e-02 2.50e+03 ... (remaining 834 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 171 2.72 - 3.27: 5297 3.27 - 3.81: 8307 3.81 - 4.36: 10078 4.36 - 4.90: 17087 Nonbonded interactions: 40940 Sorted by model distance: nonbonded pdb=" OD2 ASP A 169 " pdb="FE FE2 A 601 " model vdw 2.178 3.000 nonbonded pdb=" OH TYR A 325 " pdb=" OG1 THR A 375 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR B 325 " pdb=" OG1 THR B 375 " model vdw 2.189 3.040 nonbonded pdb=" O LEU B 343 " pdb=" OG1 THR B 347 " model vdw 2.211 3.040 nonbonded pdb=" OG SER A 379 " pdb=" NE2 HIS A 458 " model vdw 2.224 3.120 ... (remaining 40935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 98 through 186 or (resid 187 and (name N or name CA or nam \ e C or name O or name CB )) or resid 188 through 234 or (resid 235 and (name N o \ r name CA or name C or name O or name CB )) or resid 236 through 445 or (resid 4 \ 46 and (name N or name CA or name C or name O or name CB )) or resid 447 through \ 472 or (resid 473 and (name N or name CA or name C or name O or name CB )) or r \ esid 474 through 601)) selection = (chain 'B' and (resid 98 through 177 or (resid 178 and (name N or name CA or nam \ e C or name O or name CB )) or resid 179 through 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.140 Find NCS groups from input model: 0.050 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 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 : 0.003 0.048 5020 Z= 0.125 Angle : 0.581 9.618 6820 Z= 0.282 Chirality : 0.038 0.147 825 Planarity : 0.003 0.033 837 Dihedral : 17.543 88.993 1706 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.61 % Allowed : 35.90 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.34), residues: 658 helix: -0.31 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.34 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.016 0.001 TYR B 115 PHE 0.010 0.001 PHE B 215 TRP 0.012 0.001 TRP B 242 HIS 0.002 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 5020) covalent geometry : angle 0.58064 ( 6820) hydrogen bonds : bond 0.23975 ( 331) hydrogen bonds : angle 8.63038 ( 984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.188 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 103 average time/residue: 0.0657 time to fit residues: 8.9814 Evaluate side-chains 100 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.239472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.221597 restraints weight = 5229.167| |-----------------------------------------------------------------------------| r_work (start): 0.4601 rms_B_bonded: 1.34 r_work: 0.4509 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4381 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5020 Z= 0.177 Angle : 0.629 6.484 6820 Z= 0.311 Chirality : 0.041 0.219 825 Planarity : 0.004 0.033 837 Dihedral : 4.798 16.999 714 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.07 % Allowed : 31.03 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.34), residues: 658 helix: 0.04 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.33 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.021 0.002 TYR B 115 PHE 0.012 0.001 PHE A 354 TRP 0.011 0.001 TRP A 242 HIS 0.003 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 5020) covalent geometry : angle 0.62884 ( 6820) hydrogen bonds : bond 0.04080 ( 331) hydrogen bonds : angle 5.06207 ( 984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.179 Fit side-chains REVERT: B 177 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7567 (mp) REVERT: B 226 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7254 (mp) REVERT: A 214 ARG cc_start: 0.7713 (ttm110) cc_final: 0.7460 (ttm110) outliers start: 25 outliers final: 11 residues processed: 116 average time/residue: 0.0615 time to fit residues: 9.6299 Evaluate side-chains 109 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 469 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.238959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.221477 restraints weight = 5161.113| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 1.29 r_work: 0.4502 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4375 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5020 Z= 0.171 Angle : 0.610 7.754 6820 Z= 0.300 Chirality : 0.040 0.138 825 Planarity : 0.003 0.032 837 Dihedral : 4.807 15.646 711 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.68 % Allowed : 30.83 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.34), residues: 658 helix: 0.14 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.28 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.024 0.002 TYR B 115 PHE 0.012 0.001 PHE B 354 TRP 0.010 0.001 TRP B 242 HIS 0.003 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 5020) covalent geometry : angle 0.61031 ( 6820) hydrogen bonds : bond 0.03733 ( 331) hydrogen bonds : angle 4.72633 ( 984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.152 Fit side-chains REVERT: B 177 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7566 (mp) REVERT: B 226 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7159 (mp) outliers start: 28 outliers final: 13 residues processed: 119 average time/residue: 0.0650 time to fit residues: 10.3065 Evaluate side-chains 106 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 469 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.242306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.224870 restraints weight = 5179.834| |-----------------------------------------------------------------------------| r_work (start): 0.4632 rms_B_bonded: 1.29 r_work: 0.4542 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4416 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5020 Z= 0.147 Angle : 0.586 7.181 6820 Z= 0.289 Chirality : 0.041 0.255 825 Planarity : 0.003 0.033 837 Dihedral : 4.723 15.819 711 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 6.29 % Allowed : 29.01 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.34), residues: 658 helix: 0.27 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.37 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.026 0.002 TYR B 115 PHE 0.010 0.001 PHE B 354 TRP 0.010 0.001 TRP B 213 HIS 0.003 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 5020) covalent geometry : angle 0.58613 ( 6820) hydrogen bonds : bond 0.03447 ( 331) hydrogen bonds : angle 4.54472 ( 984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.172 Fit side-chains REVERT: B 177 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7670 (mp) REVERT: B 214 ARG cc_start: 0.7688 (ttm110) cc_final: 0.7406 (ttm110) REVERT: B 226 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7203 (mp) REVERT: B 398 SER cc_start: 0.7259 (OUTLIER) cc_final: 0.6948 (m) REVERT: A 185 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6963 (ttm170) outliers start: 31 outliers final: 14 residues processed: 122 average time/residue: 0.0678 time to fit residues: 10.9272 Evaluate side-chains 111 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 469 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 0.0370 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN A 457 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.245147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.227973 restraints weight = 5197.172| |-----------------------------------------------------------------------------| r_work (start): 0.4654 rms_B_bonded: 1.27 r_work: 0.4563 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4433 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5020 Z= 0.141 Angle : 0.596 8.312 6820 Z= 0.289 Chirality : 0.041 0.212 825 Planarity : 0.003 0.033 837 Dihedral : 4.650 15.562 711 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 5.68 % Allowed : 30.02 % Favored : 64.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.34), residues: 658 helix: 0.33 (0.24), residues: 526 sheet: None (None), residues: 0 loop : -1.25 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.027 0.002 TYR B 115 PHE 0.010 0.001 PHE B 236 TRP 0.010 0.001 TRP B 213 HIS 0.003 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 5020) covalent geometry : angle 0.59619 ( 6820) hydrogen bonds : bond 0.03302 ( 331) hydrogen bonds : angle 4.43891 ( 984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.181 Fit side-chains REVERT: B 177 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7706 (mp) REVERT: B 214 ARG cc_start: 0.7716 (ttm110) cc_final: 0.7406 (ttm110) REVERT: B 226 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7259 (mp) REVERT: B 438 LEU cc_start: 0.8227 (tt) cc_final: 0.7986 (tt) REVERT: A 185 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6770 (ttm170) REVERT: A 202 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7183 (tt) REVERT: A 214 ARG cc_start: 0.7358 (ttm110) cc_final: 0.7099 (ttm110) outliers start: 28 outliers final: 12 residues processed: 128 average time/residue: 0.0696 time to fit residues: 11.6147 Evaluate side-chains 108 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 47 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.239127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.221012 restraints weight = 5279.639| |-----------------------------------------------------------------------------| r_work (start): 0.4586 rms_B_bonded: 1.33 r_work: 0.4490 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4360 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 5020 Z= 0.194 Angle : 0.659 7.225 6820 Z= 0.318 Chirality : 0.044 0.291 825 Planarity : 0.003 0.033 837 Dihedral : 4.892 17.856 711 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 6.29 % Allowed : 30.22 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.34), residues: 658 helix: 0.16 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.57 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.028 0.002 TYR B 115 PHE 0.014 0.002 PHE A 159 TRP 0.012 0.001 TRP B 213 HIS 0.006 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 5020) covalent geometry : angle 0.65921 ( 6820) hydrogen bonds : bond 0.03540 ( 331) hydrogen bonds : angle 4.59746 ( 984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.180 Fit side-chains REVERT: B 98 TRP cc_start: 0.7545 (OUTLIER) cc_final: 0.7332 (m100) REVERT: B 177 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7621 (mp) REVERT: B 226 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7172 (mp) REVERT: B 438 LEU cc_start: 0.8357 (tt) cc_final: 0.8105 (tt) REVERT: A 185 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.7015 (ttm170) REVERT: A 202 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7351 (tt) outliers start: 31 outliers final: 18 residues processed: 120 average time/residue: 0.0688 time to fit residues: 10.8378 Evaluate side-chains 115 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 TRP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 13 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.243434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.226212 restraints weight = 5142.643| |-----------------------------------------------------------------------------| r_work (start): 0.4633 rms_B_bonded: 1.28 r_work: 0.4544 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4418 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5020 Z= 0.143 Angle : 0.625 9.388 6820 Z= 0.297 Chirality : 0.041 0.190 825 Planarity : 0.003 0.033 837 Dihedral : 4.734 16.382 711 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.67 % Allowed : 32.45 % Favored : 62.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.34), residues: 658 helix: 0.27 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.33 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 447 TYR 0.025 0.002 TYR B 115 PHE 0.011 0.001 PHE B 236 TRP 0.012 0.001 TRP B 213 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5020) covalent geometry : angle 0.62549 ( 6820) hydrogen bonds : bond 0.03274 ( 331) hydrogen bonds : angle 4.40983 ( 984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.206 Fit side-chains REVERT: B 177 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7687 (mp) REVERT: B 226 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7155 (mp) REVERT: B 372 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7815 (tpp) REVERT: B 438 LEU cc_start: 0.8308 (tt) cc_final: 0.8089 (tt) REVERT: A 185 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6826 (ttm170) REVERT: A 202 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7206 (tt) outliers start: 23 outliers final: 14 residues processed: 113 average time/residue: 0.0722 time to fit residues: 10.7612 Evaluate side-chains 113 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 16 optimal weight: 0.8980 chunk 63 optimal weight: 0.0060 chunk 2 optimal weight: 0.0270 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.0570 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 overall best weight: 0.3172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN A 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.247208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.230065 restraints weight = 5256.147| |-----------------------------------------------------------------------------| r_work (start): 0.4666 rms_B_bonded: 1.30 r_work: 0.4576 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4451 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5020 Z= 0.125 Angle : 0.598 7.415 6820 Z= 0.286 Chirality : 0.041 0.321 825 Planarity : 0.003 0.034 837 Dihedral : 4.562 21.298 711 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.87 % Allowed : 32.25 % Favored : 62.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.34), residues: 658 helix: 0.40 (0.24), residues: 528 sheet: None (None), residues: 0 loop : -1.27 (0.59), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.020 0.002 TYR B 115 PHE 0.011 0.001 PHE B 215 TRP 0.008 0.001 TRP B 213 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 5020) covalent geometry : angle 0.59789 ( 6820) hydrogen bonds : bond 0.03083 ( 331) hydrogen bonds : angle 4.25924 ( 984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.177 Fit side-chains REVERT: B 177 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7694 (mp) REVERT: B 226 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7118 (mp) REVERT: B 369 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7124 (tt) REVERT: B 372 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7580 (tpp) REVERT: B 438 LEU cc_start: 0.8277 (tt) cc_final: 0.7986 (tt) REVERT: A 185 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6715 (ttm170) REVERT: A 202 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7178 (tt) REVERT: A 214 ARG cc_start: 0.7423 (ttm110) cc_final: 0.7149 (ttm110) REVERT: A 438 LEU cc_start: 0.8159 (tt) cc_final: 0.7872 (tt) outliers start: 24 outliers final: 12 residues processed: 123 average time/residue: 0.0645 time to fit residues: 10.5133 Evaluate side-chains 115 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 53 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN A 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.242245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.224878 restraints weight = 5146.038| |-----------------------------------------------------------------------------| r_work (start): 0.4619 rms_B_bonded: 1.26 r_work: 0.4527 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4402 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5020 Z= 0.174 Angle : 0.655 7.997 6820 Z= 0.311 Chirality : 0.043 0.193 825 Planarity : 0.003 0.034 837 Dihedral : 4.751 20.008 711 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.87 % Allowed : 32.86 % Favored : 62.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.34), residues: 658 helix: 0.29 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.30 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 218 TYR 0.026 0.002 TYR B 115 PHE 0.014 0.002 PHE A 159 TRP 0.013 0.001 TRP B 213 HIS 0.004 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 5020) covalent geometry : angle 0.65478 ( 6820) hydrogen bonds : bond 0.03377 ( 331) hydrogen bonds : angle 4.46924 ( 984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.155 Fit side-chains REVERT: B 177 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7717 (mp) REVERT: B 226 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7169 (mp) REVERT: B 372 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7788 (tpp) REVERT: B 438 LEU cc_start: 0.8298 (tt) cc_final: 0.8008 (tt) REVERT: A 185 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6846 (ttm170) REVERT: A 202 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7370 (tt) REVERT: A 214 ARG cc_start: 0.7506 (ttm110) cc_final: 0.7201 (ttm110) outliers start: 24 outliers final: 15 residues processed: 119 average time/residue: 0.0676 time to fit residues: 10.7099 Evaluate side-chains 118 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 61 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.239999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.222339 restraints weight = 5194.733| |-----------------------------------------------------------------------------| r_work (start): 0.4597 rms_B_bonded: 1.27 r_work: 0.4502 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4374 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5020 Z= 0.200 Angle : 0.708 9.807 6820 Z= 0.334 Chirality : 0.045 0.330 825 Planarity : 0.004 0.033 837 Dihedral : 4.978 19.513 711 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 5.68 % Allowed : 31.85 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.34), residues: 658 helix: 0.13 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.32 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.026 0.002 TYR B 115 PHE 0.015 0.002 PHE A 159 TRP 0.017 0.002 TRP B 213 HIS 0.006 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 5020) covalent geometry : angle 0.70808 ( 6820) hydrogen bonds : bond 0.03536 ( 331) hydrogen bonds : angle 4.61911 ( 984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.169 Fit side-chains REVERT: B 177 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7672 (mp) REVERT: B 226 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7170 (mp) REVERT: B 355 LEU cc_start: 0.7065 (tt) cc_final: 0.6831 (tt) REVERT: B 372 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7858 (tpp) REVERT: B 438 LEU cc_start: 0.8307 (tt) cc_final: 0.8096 (tt) REVERT: A 177 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7505 (mp) REVERT: A 185 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6859 (ttm170) REVERT: A 202 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7472 (tt) outliers start: 28 outliers final: 18 residues processed: 113 average time/residue: 0.0654 time to fit residues: 9.8214 Evaluate side-chains 120 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.237535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.219546 restraints weight = 5229.668| |-----------------------------------------------------------------------------| r_work (start): 0.4573 rms_B_bonded: 1.30 r_work: 0.4476 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4348 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5020 Z= 0.211 Angle : 0.709 8.838 6820 Z= 0.336 Chirality : 0.044 0.188 825 Planarity : 0.004 0.033 837 Dihedral : 5.091 19.924 711 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.87 % Allowed : 32.86 % Favored : 62.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.34), residues: 658 helix: 0.06 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.38 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.030 0.002 TYR B 115 PHE 0.017 0.002 PHE A 159 TRP 0.014 0.001 TRP B 213 HIS 0.005 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 5020) covalent geometry : angle 0.70871 ( 6820) hydrogen bonds : bond 0.03594 ( 331) hydrogen bonds : angle 4.69257 ( 984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1322.11 seconds wall clock time: 23 minutes 19.55 seconds (1399.55 seconds total)