Starting phenix.real_space_refine on Thu Jul 24 01:53:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9il4_60664/07_2025/9il4_60664.cif Found real_map, /net/cci-nas-00/data/ceres_data/9il4_60664/07_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_60664/07_2025/9il4_60664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9il4_60664/07_2025/9il4_60664.map" model { file = "/net/cci-nas-00/data/ceres_data/9il4_60664/07_2025/9il4_60664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9il4_60664/07_2025/9il4_60664.cif" } resolution = 3.33 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= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG: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: 3.54, per 1000 atoms: 0.72 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: 1.30 Conformation dependent library (CDL) restraints added in 630.6 milliseconds 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: 0.54 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: 1.29 Time building geometry restraints manager: 1.48 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 475 or resid 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 475 or resid 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: 0.680 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.590 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.490 ------------------------------------------------------------------------------- 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 (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: -0.95 (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 TRP 0.012 0.001 TRP B 242 HIS 0.002 0.001 HIS A 449 PHE 0.010 0.001 PHE B 215 TYR 0.016 0.001 TYR B 115 ARG 0.002 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.23975 ( 331) hydrogen bonds : angle 8.63038 ( 984) covalent geometry : bond 0.00283 ( 5020) covalent geometry : angle 0.58064 ( 6820) *********************** 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 : 0.475 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 103 average time/residue: 0.1436 time to fit residues: 19.5580 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 : 0.512 ------------------------------------------------------------------------------- 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 55 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 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** B 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.239235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.221522 restraints weight = 5138.294| |-----------------------------------------------------------------------------| r_work (start): 0.4602 rms_B_bonded: 1.32 r_work: 0.4514 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4385 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5020 Z= 0.176 Angle : 0.627 6.487 6820 Z= 0.310 Chirality : 0.041 0.217 825 Planarity : 0.004 0.033 837 Dihedral : 4.793 17.084 714 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.48 % Allowed : 30.63 % 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 (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: -0.49 (0.34), residues: 658 helix: 0.05 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.33 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 242 HIS 0.003 0.001 HIS A 449 PHE 0.012 0.001 PHE A 354 TYR 0.022 0.002 TYR B 115 ARG 0.002 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 331) hydrogen bonds : angle 5.03337 ( 984) covalent geometry : bond 0.00403 ( 5020) covalent geometry : angle 0.62691 ( 6820) *********************** 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 128 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.540 Fit side-chains REVERT: B 177 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7563 (mp) REVERT: B 226 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7252 (mp) REVERT: A 214 ARG cc_start: 0.7720 (ttm110) cc_final: 0.7464 (ttm110) outliers start: 27 outliers final: 8 residues processed: 118 average time/residue: 0.1337 time to fit residues: 21.1522 Evaluate side-chains 106 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 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 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 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4709 r_free = 0.4709 target = 0.240526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.223242 restraints weight = 5188.794| |-----------------------------------------------------------------------------| r_work (start): 0.4611 rms_B_bonded: 1.29 r_work: 0.4517 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4394 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1579 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= 0.159 Angle : 0.597 7.680 6820 Z= 0.294 Chirality : 0.040 0.135 825 Planarity : 0.003 0.032 837 Dihedral : 4.739 15.529 711 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.26 % Allowed : 31.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.34), residues: 658 helix: 0.20 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.28 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 242 HIS 0.003 0.001 HIS A 449 PHE 0.011 0.001 PHE B 354 TYR 0.024 0.002 TYR B 115 ARG 0.005 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 331) hydrogen bonds : angle 4.68681 ( 984) covalent geometry : bond 0.00368 ( 5020) covalent geometry : angle 0.59693 ( 6820) *********************** 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 123 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.527 Fit side-chains REVERT: B 177 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7559 (mp) REVERT: B 226 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7148 (mp) REVERT: B 438 LEU cc_start: 0.8281 (tt) cc_final: 0.8029 (tt) outliers start: 21 outliers final: 11 residues processed: 115 average time/residue: 0.1438 time to fit residues: 22.0909 Evaluate side-chains 105 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 206 LEU Chi-restraints excluded: chain B residue 226 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 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 41 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** A 406 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.234498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.216103 restraints weight = 5232.166| |-----------------------------------------------------------------------------| r_work (start): 0.4542 rms_B_bonded: 1.33 r_work: 0.4446 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4320 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5020 Z= 0.243 Angle : 0.698 9.436 6820 Z= 0.339 Chirality : 0.044 0.258 825 Planarity : 0.004 0.032 837 Dihedral : 5.124 17.067 711 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % 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 (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 (0.34), residues: 658 helix: -0.02 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.43 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 242 HIS 0.005 0.001 HIS A 449 PHE 0.015 0.002 PHE A 159 TYR 0.031 0.002 TYR B 115 ARG 0.004 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 331) hydrogen bonds : angle 4.87280 ( 984) covalent geometry : bond 0.00573 ( 5020) covalent geometry : angle 0.69805 ( 6820) *********************** 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 128 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.465 Fit side-chains REVERT: B 177 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7515 (mp) REVERT: B 214 ARG cc_start: 0.7787 (ttm110) cc_final: 0.7482 (ttm110) REVERT: B 226 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7244 (mp) REVERT: B 398 SER cc_start: 0.7379 (OUTLIER) cc_final: 0.7061 (m) REVERT: A 185 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7118 (ttm170) REVERT: A 449 HIS cc_start: 0.6445 (OUTLIER) cc_final: 0.5475 (m-70) outliers start: 31 outliers final: 17 residues processed: 120 average time/residue: 0.1540 time to fit residues: 23.9229 Evaluate side-chains 113 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 206 LEU 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 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 433 MET Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 467 LEU 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 56 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 303 ASN A 457 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.239313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.221718 restraints weight = 5212.463| |-----------------------------------------------------------------------------| r_work (start): 0.4595 rms_B_bonded: 1.29 r_work: 0.4503 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4376 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5020 Z= 0.167 Angle : 0.629 8.309 6820 Z= 0.303 Chirality : 0.041 0.183 825 Planarity : 0.003 0.032 837 Dihedral : 4.942 16.547 711 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 6.69 % Allowed : 28.19 % Favored : 65.11 % 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: -0.40 (0.34), residues: 658 helix: 0.06 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.10 (0.62), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 242 HIS 0.004 0.001 HIS A 449 PHE 0.011 0.001 PHE B 354 TYR 0.028 0.002 TYR B 115 ARG 0.003 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 331) hydrogen bonds : angle 4.61809 ( 984) covalent geometry : bond 0.00395 ( 5020) covalent geometry : angle 0.62853 ( 6820) *********************** 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 133 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.472 Fit side-chains REVERT: B 98 TRP cc_start: 0.7549 (OUTLIER) cc_final: 0.7324 (m100) REVERT: B 177 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7631 (mp) REVERT: B 214 ARG cc_start: 0.7757 (ttm110) cc_final: 0.7382 (ttm110) REVERT: B 226 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7254 (mp) REVERT: B 398 SER cc_start: 0.7217 (OUTLIER) cc_final: 0.6895 (m) REVERT: A 185 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6992 (ttm170) REVERT: A 438 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7957 (tt) REVERT: A 449 HIS cc_start: 0.5972 (OUTLIER) cc_final: 0.5074 (m-70) outliers start: 33 outliers final: 16 residues processed: 123 average time/residue: 0.1504 time to fit residues: 24.0856 Evaluate side-chains 116 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 TRP 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 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 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 438 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 467 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 39 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 0.0970 chunk 26 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.4710 r_free = 0.4710 target = 0.240663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.222988 restraints weight = 5235.383| |-----------------------------------------------------------------------------| r_work (start): 0.4604 rms_B_bonded: 1.30 r_work: 0.4511 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.4385 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5020 Z= 0.161 Angle : 0.617 8.244 6820 Z= 0.301 Chirality : 0.042 0.295 825 Planarity : 0.003 0.033 837 Dihedral : 4.876 17.371 711 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 6.09 % Allowed : 29.61 % 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 (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: -0.24 (0.34), residues: 658 helix: 0.22 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.26 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 213 HIS 0.011 0.001 HIS A 458 PHE 0.011 0.002 PHE B 236 TYR 0.025 0.002 TYR B 115 ARG 0.002 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 331) hydrogen bonds : angle 4.56184 ( 984) covalent geometry : bond 0.00380 ( 5020) covalent geometry : angle 0.61708 ( 6820) *********************** 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 131 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.509 Fit side-chains REVERT: B 98 TRP cc_start: 0.7570 (OUTLIER) cc_final: 0.7367 (m100) REVERT: B 157 LEU cc_start: 0.7255 (mp) cc_final: 0.7046 (mp) REVERT: B 177 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7638 (mp) REVERT: B 226 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7222 (mp) REVERT: B 369 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7149 (tt) REVERT: B 438 LEU cc_start: 0.8310 (tt) cc_final: 0.8068 (tt) REVERT: A 185 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6989 (ttm170) REVERT: A 202 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7223 (tt) REVERT: A 438 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7916 (tt) REVERT: A 449 HIS cc_start: 0.5843 (OUTLIER) cc_final: 0.4968 (m-70) outliers start: 30 outliers final: 18 residues processed: 120 average time/residue: 0.1431 time to fit residues: 22.6867 Evaluate side-chains 118 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 369 LEU Chi-restraints excluded: chain B residue 417 SER 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 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 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 438 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 467 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 61 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 0.0070 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 37 optimal weight: 0.0270 chunk 40 optimal weight: 0.7980 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 = 0.242482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.225130 restraints weight = 5126.207| |-----------------------------------------------------------------------------| r_work (start): 0.4633 rms_B_bonded: 1.29 r_work: 0.4544 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4417 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5020 Z= 0.137 Angle : 0.599 7.546 6820 Z= 0.290 Chirality : 0.040 0.182 825 Planarity : 0.003 0.033 837 Dihedral : 4.730 16.885 711 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 6.49 % Allowed : 30.22 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.34), residues: 658 helix: 0.38 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -1.18 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 242 HIS 0.007 0.001 HIS A 458 PHE 0.012 0.001 PHE B 403 TYR 0.023 0.002 TYR B 115 ARG 0.002 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 331) hydrogen bonds : angle 4.41492 ( 984) covalent geometry : bond 0.00319 ( 5020) covalent geometry : angle 0.59850 ( 6820) *********************** 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 136 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.447 Fit side-chains REVERT: B 157 LEU cc_start: 0.7208 (mp) cc_final: 0.6997 (mp) REVERT: B 177 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7677 (mp) REVERT: B 226 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7098 (mp) REVERT: B 369 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7100 (tt) REVERT: B 438 LEU cc_start: 0.8276 (tt) cc_final: 0.8031 (tt) REVERT: A 185 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6813 (ttm170) REVERT: A 202 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7109 (tt) REVERT: A 438 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7901 (tt) outliers start: 32 outliers final: 13 residues processed: 128 average time/residue: 0.1413 time to fit residues: 23.7775 Evaluate side-chains 116 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 369 LEU 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 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 438 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: 0.7980 chunk 48 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.240562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.222876 restraints weight = 5206.395| |-----------------------------------------------------------------------------| r_work (start): 0.4601 rms_B_bonded: 1.31 r_work: 0.4505 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4379 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2115 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 : 0.639 7.759 6820 Z= 0.310 Chirality : 0.044 0.325 825 Planarity : 0.003 0.034 837 Dihedral : 4.853 20.376 711 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.87 % Allowed : 32.66 % 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 (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: -0.26 (0.34), residues: 658 helix: 0.25 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.43 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 213 HIS 0.004 0.001 HIS A 449 PHE 0.013 0.002 PHE A 159 TYR 0.025 0.002 TYR B 115 ARG 0.003 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 331) hydrogen bonds : angle 4.49661 ( 984) covalent geometry : bond 0.00413 ( 5020) covalent geometry : angle 0.63905 ( 6820) *********************** 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 124 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.973 Fit side-chains REVERT: B 157 LEU cc_start: 0.7217 (mp) cc_final: 0.6995 (mp) REVERT: B 177 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7658 (mp) REVERT: B 226 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7154 (mp) REVERT: B 438 LEU cc_start: 0.8322 (tt) cc_final: 0.8074 (tt) REVERT: A 157 LEU cc_start: 0.7185 (mp) cc_final: 0.6981 (mp) REVERT: A 185 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6870 (ttm170) REVERT: A 438 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7949 (tt) outliers start: 24 outliers final: 14 residues processed: 117 average time/residue: 0.1921 time to fit residues: 29.7155 Evaluate side-chains 116 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 438 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 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 = 0.4736 r_free = 0.4736 target = 0.244108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.227156 restraints weight = 5130.653| |-----------------------------------------------------------------------------| r_work (start): 0.4635 rms_B_bonded: 1.26 r_work: 0.4544 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4418 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5020 Z= 0.144 Angle : 0.613 7.333 6820 Z= 0.295 Chirality : 0.041 0.178 825 Planarity : 0.003 0.034 837 Dihedral : 4.729 20.784 711 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.87 % Allowed : 32.45 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.34), residues: 658 helix: 0.27 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.12 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 242 HIS 0.003 0.001 HIS A 449 PHE 0.012 0.001 PHE B 403 TYR 0.024 0.002 TYR B 115 ARG 0.003 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.03265 ( 331) hydrogen bonds : angle 4.40417 ( 984) covalent geometry : bond 0.00340 ( 5020) covalent geometry : angle 0.61325 ( 6820) *********************** 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 124 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.675 Fit side-chains REVERT: B 157 LEU cc_start: 0.7206 (mp) cc_final: 0.6997 (mp) REVERT: B 177 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7678 (mp) REVERT: B 226 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7130 (mp) REVERT: B 372 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7725 (tpp) REVERT: B 438 LEU cc_start: 0.8325 (tt) cc_final: 0.8067 (tt) REVERT: A 185 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6816 (ttm170) REVERT: A 214 ARG cc_start: 0.7450 (ttm110) cc_final: 0.7165 (ttm110) REVERT: A 438 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7911 (tt) outliers start: 24 outliers final: 15 residues processed: 116 average time/residue: 0.2125 time to fit residues: 32.2564 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 : 1.646 ------------------------------------------------------------------------------- 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 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 204 LEU Chi-restraints excluded: chain A residue 228 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 438 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 24 optimal weight: 0.0870 chunk 59 optimal weight: 0.0370 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 0.0170 overall best weight: 0.3074 ------------------------------------------------------------------------------- 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 B 248 GLN A 406 GLN A 446 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.248378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.231567 restraints weight = 5141.015| |-----------------------------------------------------------------------------| r_work (start): 0.4670 rms_B_bonded: 1.25 r_work: 0.4581 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4454 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5020 Z= 0.127 Angle : 0.614 7.230 6820 Z= 0.291 Chirality : 0.041 0.340 825 Planarity : 0.003 0.035 837 Dihedral : 4.556 21.298 711 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.07 % Allowed : 32.45 % 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 (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: 0.06 (0.34), residues: 658 helix: 0.39 (0.24), residues: 534 sheet: None (None), residues: 0 loop : -1.01 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 242 HIS 0.002 0.001 HIS A 200 PHE 0.012 0.001 PHE B 403 TYR 0.021 0.002 TYR B 115 ARG 0.003 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.03104 ( 331) hydrogen bonds : angle 4.29121 ( 984) covalent geometry : bond 0.00290 ( 5020) covalent geometry : angle 0.61357 ( 6820) ********************** 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 128 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.669 Fit side-chains REVERT: B 177 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7656 (mp) REVERT: B 226 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7128 (mp) REVERT: B 438 LEU cc_start: 0.8280 (tt) cc_final: 0.8004 (tt) REVERT: A 157 LEU cc_start: 0.7140 (mp) cc_final: 0.6939 (mp) REVERT: A 177 LEU cc_start: 0.7912 (mp) cc_final: 0.7694 (mt) REVERT: A 185 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6733 (ttm170) REVERT: A 214 ARG cc_start: 0.7357 (ttm110) cc_final: 0.7102 (ttm110) REVERT: A 438 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7909 (tt) outliers start: 25 outliers final: 15 residues processed: 119 average time/residue: 0.1464 time to fit residues: 24.2828 Evaluate side-chains 117 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 398 SER 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 194 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 350 LEU 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 438 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: 2.9990 chunk 60 optimal weight: 0.0980 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4738 r_free = 0.4738 target = 0.244150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.227020 restraints weight = 5174.464| |-----------------------------------------------------------------------------| r_work (start): 0.4637 rms_B_bonded: 1.26 r_work: 0.4544 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4417 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2471 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= 0.154 Angle : 0.658 10.211 6820 Z= 0.309 Chirality : 0.042 0.175 825 Planarity : 0.003 0.034 837 Dihedral : 4.671 19.492 711 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.46 % Allowed : 33.67 % Favored : 61.87 % 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: -0.03 (0.34), residues: 658 helix: 0.36 (0.24), residues: 528 sheet: None (None), residues: 0 loop : -1.21 (0.59), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 213 HIS 0.003 0.001 HIS A 449 PHE 0.012 0.002 PHE B 403 TYR 0.023 0.002 TYR B 115 ARG 0.003 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 331) hydrogen bonds : angle 4.40041 ( 984) covalent geometry : bond 0.00363 ( 5020) covalent geometry : angle 0.65817 ( 6820) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2948.86 seconds wall clock time: 53 minutes 49.85 seconds (3229.85 seconds total)