Starting phenix.real_space_refine on Mon Feb 10 22:43:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvm_34132/02_2025/7yvm_34132.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvm_34132/02_2025/7yvm_34132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvm_34132/02_2025/7yvm_34132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvm_34132/02_2025/7yvm_34132.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvm_34132/02_2025/7yvm_34132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvm_34132/02_2025/7yvm_34132.cif" } resolution = 3.5 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 1991 2.51 5 N 528 2.21 5 O 591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3126 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 821 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 870 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1435 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 80 Time building chain proxies: 4.53, per 1000 atoms: 1.45 Number of scatterers: 3126 At special positions: 0 Unit cell: (62.32, 72.16, 100.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 591 8.00 N 528 7.00 C 1991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.06 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.09 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 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: 0.59 Conformation dependent library (CDL) restraints added in 370.9 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 9.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.134A pdb=" N SER A 83 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 86 through 90 removed outlier: 4.139A pdb=" N THR C 90 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.838A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 3.821A pdb=" N GLU A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.680A pdb=" N LEU A 11 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 85 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU A 33 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TYR A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.998A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.998A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR C 107 " --> pdb=" O ARG C 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.667A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 106 hydrogen bonds defined for protein. 252 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: 0.82 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 505 1.31 - 1.44: 942 1.44 - 1.58: 1737 1.58 - 1.71: 0 1.71 - 1.85: 20 Bond restraints: 3204 Sorted by residual: bond pdb=" C TYR C 33 " pdb=" O TYR C 33 " ideal model delta sigma weight residual 1.235 1.172 0.063 1.26e-02 6.30e+03 2.50e+01 bond pdb=" C PRO A 95 " pdb=" O PRO A 95 " ideal model delta sigma weight residual 1.240 1.186 0.055 1.12e-02 7.97e+03 2.39e+01 bond pdb=" N GLY A 101 " pdb=" CA GLY A 101 " ideal model delta sigma weight residual 1.442 1.479 -0.037 7.70e-03 1.69e+04 2.30e+01 bond pdb=" CA ASN A 93 " pdb=" C ASN A 93 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.28e-02 6.10e+03 2.16e+01 bond pdb=" C THR A 99 " pdb=" O THR A 99 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.13e-02 7.83e+03 1.90e+01 ... (remaining 3199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 4287 4.04 - 8.08: 70 8.08 - 12.12: 8 12.12 - 16.16: 1 16.16 - 20.20: 3 Bond angle restraints: 4369 Sorted by residual: angle pdb=" C PRO A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta sigma weight residual 119.84 138.11 -18.27 1.25e+00 6.40e-01 2.14e+02 angle pdb=" N PRO B 521 " pdb=" CA PRO B 521 " pdb=" C PRO B 521 " ideal model delta sigma weight residual 112.33 92.13 20.20 1.87e+00 2.86e-01 1.17e+02 angle pdb=" C TYR A 98 " pdb=" CA TYR A 98 " pdb=" CB TYR A 98 " ideal model delta sigma weight residual 109.99 93.12 16.87 1.61e+00 3.86e-01 1.10e+02 angle pdb=" C ARG C 97 " pdb=" CA ARG C 97 " pdb=" CB ARG C 97 " ideal model delta sigma weight residual 111.23 99.22 12.01 1.68e+00 3.54e-01 5.11e+01 angle pdb=" C ARG B 454 " pdb=" CA ARG B 454 " pdb=" CB ARG B 454 " ideal model delta sigma weight residual 110.19 99.37 10.82 1.62e+00 3.81e-01 4.46e+01 ... (remaining 4364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.11: 1776 24.11 - 48.22: 86 48.22 - 72.32: 10 72.32 - 96.43: 0 96.43 - 120.54: 1 Dihedral angle restraints: 1873 sinusoidal: 667 harmonic: 1206 Sorted by residual: dihedral pdb=" CA PRO A 95 " pdb=" C PRO A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual -180.00 -59.46 -120.54 0 5.00e+00 4.00e-02 5.81e+02 dihedral pdb=" C TRP A 94 " pdb=" N TRP A 94 " pdb=" CA TRP A 94 " pdb=" CB TRP A 94 " ideal model delta harmonic sigma weight residual -122.60 -151.47 28.87 0 2.50e+00 1.60e-01 1.33e+02 dihedral pdb=" N TRP A 94 " pdb=" C TRP A 94 " pdb=" CA TRP A 94 " pdb=" CB TRP A 94 " ideal model delta harmonic sigma weight residual 122.80 151.58 -28.78 0 2.50e+00 1.60e-01 1.33e+02 ... (remaining 1870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.252: 476 0.252 - 0.504: 5 0.504 - 0.757: 0 0.757 - 1.009: 0 1.009 - 1.261: 1 Chirality restraints: 482 Sorted by residual: chirality pdb=" CA TRP A 94 " pdb=" N TRP A 94 " pdb=" C TRP A 94 " pdb=" CB TRP A 94 " both_signs ideal model delta sigma weight residual False 2.51 1.25 1.26 2.00e-01 2.50e+01 3.97e+01 chirality pdb=" CA CYS C 95 " pdb=" N CYS C 95 " pdb=" C CYS C 95 " pdb=" CB CYS C 95 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" CA TYR A 98 " pdb=" N TYR A 98 " pdb=" C TYR A 98 " pdb=" CB TYR A 98 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 479 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 90 " -0.036 2.00e-02 2.50e+03 7.38e-02 5.45e+01 pdb=" C GLN A 90 " 0.128 2.00e-02 2.50e+03 pdb=" O GLN A 90 " -0.047 2.00e-02 2.50e+03 pdb=" N TYR A 91 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 94 " -0.086 5.00e-02 4.00e+02 1.34e-01 2.87e+01 pdb=" N PRO A 95 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 94 " 0.049 2.00e-02 2.50e+03 2.66e-02 1.77e+01 pdb=" CG TRP A 94 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 94 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 94 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 94 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 94 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 94 " -0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 94 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 94 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A 94 " 0.017 2.00e-02 2.50e+03 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 205 2.71 - 3.26: 3153 3.26 - 3.81: 4790 3.81 - 4.35: 5932 4.35 - 4.90: 9876 Nonbonded interactions: 23956 Sorted by model distance: nonbonded pdb=" OH TYR A 98 " pdb=" OG1 THR C 105 " model vdw 2.166 3.040 nonbonded pdb=" O SER A 77 " pdb=" NE2 GLN A 79 " model vdw 2.275 3.120 nonbonded pdb=" NH1 ARG C 66 " pdb=" O ASN C 83 " model vdw 2.349 3.120 nonbonded pdb=" O LEU B 518 " pdb=" C HIS B 519 " model vdw 2.357 3.270 nonbonded pdb=" SD MET A 4 " pdb=" OE1 GLN A 90 " model vdw 2.363 3.400 ... (remaining 23951 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.100 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.100 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.009 0.063 3204 Z= 0.602 Angle : 1.377 20.197 4369 Z= 0.858 Chirality : 0.092 1.261 482 Planarity : 0.009 0.134 566 Dihedral : 13.483 120.539 1091 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 28.59 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.94 % Favored : 90.58 % Rotamer: Outliers : 1.57 % Allowed : 7.55 % Favored : 90.88 % Cbeta Deviations : 1.57 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.34), residues: 414 helix: -4.90 (0.26), residues: 21 sheet: -1.69 (0.41), residues: 127 loop : -3.36 (0.31), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.008 TRP C 47 HIS 0.001 0.000 HIS B 505 PHE 0.034 0.003 PHE B 347 TYR 0.044 0.003 TYR B 380 ARG 0.010 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8297 (mp) cc_final: 0.7834 (mt) REVERT: C 59 TYR cc_start: 0.8050 (m-80) cc_final: 0.7160 (m-80) REVERT: B 432 CYS cc_start: 0.5883 (p) cc_final: 0.4893 (p) outliers start: 5 outliers final: 3 residues processed: 106 average time/residue: 0.1734 time to fit residues: 21.7522 Evaluate side-chains 60 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 95 PRO Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 493 GLN B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.147668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.131103 restraints weight = 6576.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.134077 restraints weight = 3775.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.135991 restraints weight = 2553.338| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 3204 Z= 0.251 Angle : 0.758 10.577 4369 Z= 0.391 Chirality : 0.048 0.245 482 Planarity : 0.006 0.083 566 Dihedral : 5.957 54.084 466 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.35 % Favored : 95.17 % Rotamer: Outliers : 3.46 % Allowed : 16.04 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.38), residues: 414 helix: -3.55 (0.75), residues: 23 sheet: -1.20 (0.41), residues: 133 loop : -2.12 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 47 HIS 0.001 0.000 HIS B 519 PHE 0.017 0.002 PHE B 371 TYR 0.020 0.002 TYR A 49 ARG 0.003 0.001 ARG C 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8313 (mp) cc_final: 0.7887 (mt) REVERT: C 34 MET cc_start: 0.8085 (mmm) cc_final: 0.7823 (mmm) REVERT: C 59 TYR cc_start: 0.7935 (m-80) cc_final: 0.7106 (m-80) REVERT: B 418 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8440 (mt) outliers start: 11 outliers final: 5 residues processed: 73 average time/residue: 0.1725 time to fit residues: 14.9891 Evaluate side-chains 66 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 418 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.0270 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** A 92 ASN ** 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 = 0.3957 r_free = 0.3957 target = 0.142592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.126236 restraints weight = 6599.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.129143 restraints weight = 3757.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.131085 restraints weight = 2534.312| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 3204 Z= 0.355 Angle : 0.783 12.611 4369 Z= 0.405 Chirality : 0.048 0.301 482 Planarity : 0.006 0.070 566 Dihedral : 5.645 54.850 458 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.00 % Favored : 92.75 % Rotamer: Outliers : 4.72 % Allowed : 20.13 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.39), residues: 414 helix: -2.16 (1.02), residues: 21 sheet: -0.73 (0.43), residues: 129 loop : -1.91 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 47 HIS 0.001 0.000 HIS B 519 PHE 0.033 0.002 PHE B 392 TYR 0.017 0.002 TYR A 49 ARG 0.005 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8440 (mp) cc_final: 0.7989 (mt) REVERT: A 70 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6966 (mp0) REVERT: C 59 TYR cc_start: 0.7937 (m-80) cc_final: 0.7128 (m-80) REVERT: B 351 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.6775 (t80) REVERT: B 436 TRP cc_start: 0.6951 (OUTLIER) cc_final: 0.6041 (m-10) outliers start: 15 outliers final: 7 residues processed: 73 average time/residue: 0.1829 time to fit residues: 15.7114 Evaluate side-chains 66 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 436 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 0.0050 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.143714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.127189 restraints weight = 6623.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.130099 restraints weight = 3779.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.132050 restraints weight = 2552.593| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 3204 Z= 0.230 Angle : 0.705 8.958 4369 Z= 0.364 Chirality : 0.045 0.248 482 Planarity : 0.006 0.077 566 Dihedral : 5.232 47.825 458 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.35 % Allowed : 21.07 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.40), residues: 414 helix: -2.64 (0.88), residues: 21 sheet: -0.41 (0.43), residues: 142 loop : -1.47 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 94 HIS 0.001 0.000 HIS B 505 PHE 0.018 0.002 PHE B 392 TYR 0.015 0.001 TYR A 49 ARG 0.002 0.000 ARG C 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8506 (mp) cc_final: 0.8049 (mt) REVERT: A 24 ARG cc_start: 0.7768 (ttp-110) cc_final: 0.7424 (ttp80) REVERT: A 70 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7081 (mp0) REVERT: A 79 GLN cc_start: 0.7110 (mp10) cc_final: 0.6573 (mp10) REVERT: C 43 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8238 (ttpt) REVERT: C 59 TYR cc_start: 0.7905 (m-80) cc_final: 0.7160 (m-80) REVERT: B 351 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.6756 (t80) REVERT: B 436 TRP cc_start: 0.6787 (OUTLIER) cc_final: 0.5848 (m-10) outliers start: 17 outliers final: 10 residues processed: 73 average time/residue: 0.1618 time to fit residues: 14.2698 Evaluate side-chains 69 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 17 optimal weight: 0.0470 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.141757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.125315 restraints weight = 6659.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.128115 restraints weight = 3858.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.130037 restraints weight = 2646.217| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 3204 Z= 0.315 Angle : 0.743 9.797 4369 Z= 0.388 Chirality : 0.046 0.275 482 Planarity : 0.006 0.071 566 Dihedral : 5.388 50.721 458 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 5.97 % Allowed : 23.58 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.40), residues: 414 helix: -1.70 (0.99), residues: 21 sheet: -0.31 (0.43), residues: 144 loop : -1.84 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 353 HIS 0.001 0.001 HIS B 505 PHE 0.034 0.003 PHE B 392 TYR 0.014 0.002 TYR A 49 ARG 0.004 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8550 (mp) cc_final: 0.8076 (mt) REVERT: A 24 ARG cc_start: 0.7849 (ttp-110) cc_final: 0.7510 (ttp80) REVERT: A 79 GLN cc_start: 0.7136 (mp10) cc_final: 0.6532 (mp10) REVERT: C 59 TYR cc_start: 0.7951 (m-80) cc_final: 0.7209 (m-80) REVERT: B 351 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.6982 (t80) REVERT: B 436 TRP cc_start: 0.6994 (OUTLIER) cc_final: 0.6091 (m-10) outliers start: 19 outliers final: 13 residues processed: 74 average time/residue: 0.1771 time to fit residues: 15.6117 Evaluate side-chains 70 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.142599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.125364 restraints weight = 6736.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.128284 restraints weight = 3863.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.130289 restraints weight = 2632.534| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3204 Z= 0.277 Angle : 0.723 11.980 4369 Z= 0.374 Chirality : 0.045 0.275 482 Planarity : 0.005 0.067 566 Dihedral : 5.227 48.354 458 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 7.23 % Allowed : 22.33 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.40), residues: 414 helix: -1.20 (1.27), residues: 15 sheet: -0.30 (0.42), residues: 146 loop : -1.75 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 353 HIS 0.001 0.000 HIS B 505 PHE 0.022 0.002 PHE B 392 TYR 0.014 0.001 TYR A 49 ARG 0.003 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8670 (mp) cc_final: 0.8134 (mt) REVERT: A 24 ARG cc_start: 0.7849 (ttp-110) cc_final: 0.7640 (tmm-80) REVERT: A 79 GLN cc_start: 0.7105 (mp10) cc_final: 0.6490 (mp10) REVERT: C 59 TYR cc_start: 0.8011 (m-80) cc_final: 0.7304 (m-80) REVERT: B 351 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.6982 (t80) REVERT: B 436 TRP cc_start: 0.6998 (OUTLIER) cc_final: 0.6144 (m-10) outliers start: 23 outliers final: 15 residues processed: 74 average time/residue: 0.1544 time to fit residues: 13.8654 Evaluate side-chains 69 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 35 optimal weight: 0.0470 chunk 2 optimal weight: 3.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** 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 = 0.3926 r_free = 0.3926 target = 0.142217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.124781 restraints weight = 6541.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.127785 restraints weight = 3810.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.129799 restraints weight = 2600.310| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 3204 Z= 0.286 Angle : 0.737 10.460 4369 Z= 0.381 Chirality : 0.045 0.271 482 Planarity : 0.005 0.067 566 Dihedral : 5.290 47.781 458 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 6.29 % Allowed : 22.64 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.41), residues: 414 helix: -1.56 (1.26), residues: 15 sheet: -0.45 (0.41), residues: 156 loop : -1.75 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 47 HIS 0.001 0.000 HIS B 505 PHE 0.028 0.002 PHE B 392 TYR 0.013 0.001 TYR A 49 ARG 0.003 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8698 (mp) cc_final: 0.8137 (mt) REVERT: A 79 GLN cc_start: 0.7069 (mp10) cc_final: 0.6487 (mp10) REVERT: A 82 ASP cc_start: 0.8347 (t0) cc_final: 0.8128 (t0) REVERT: C 6 GLU cc_start: 0.7967 (mp0) cc_final: 0.7761 (mp0) REVERT: C 59 TYR cc_start: 0.8068 (m-80) cc_final: 0.7317 (m-80) REVERT: B 351 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.7014 (t80) REVERT: B 436 TRP cc_start: 0.7106 (OUTLIER) cc_final: 0.6145 (m-10) outliers start: 20 outliers final: 17 residues processed: 71 average time/residue: 0.1657 time to fit residues: 14.0393 Evaluate side-chains 72 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.0980 chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** 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 = 0.3957 r_free = 0.3957 target = 0.143993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.126058 restraints weight = 6571.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.128929 restraints weight = 3891.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.130894 restraints weight = 2714.221| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3204 Z= 0.233 Angle : 0.716 11.800 4369 Z= 0.367 Chirality : 0.045 0.268 482 Planarity : 0.005 0.062 566 Dihedral : 4.961 45.055 458 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 6.60 % Allowed : 23.58 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.40), residues: 414 helix: -1.23 (1.30), residues: 15 sheet: -0.25 (0.43), residues: 146 loop : -1.74 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.001 0.000 HIS B 505 PHE 0.024 0.002 PHE B 392 TYR 0.013 0.001 TYR A 49 ARG 0.005 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8690 (mp) cc_final: 0.8178 (mt) REVERT: A 24 ARG cc_start: 0.8064 (tmm-80) cc_final: 0.7714 (ttp80) REVERT: A 79 GLN cc_start: 0.7015 (mp10) cc_final: 0.6434 (mp10) REVERT: A 82 ASP cc_start: 0.8361 (t0) cc_final: 0.8134 (t0) REVERT: C 59 TYR cc_start: 0.8033 (m-80) cc_final: 0.7324 (m-80) REVERT: B 351 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.6841 (t80) REVERT: B 374 PHE cc_start: 0.4086 (m-10) cc_final: 0.3464 (m-80) REVERT: B 436 TRP cc_start: 0.7004 (OUTLIER) cc_final: 0.5932 (m-10) REVERT: B 505 HIS cc_start: 0.7003 (OUTLIER) cc_final: 0.6600 (m90) outliers start: 21 outliers final: 17 residues processed: 78 average time/residue: 0.1728 time to fit residues: 15.9810 Evaluate side-chains 77 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 505 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 0.0170 chunk 30 optimal weight: 0.6980 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.144278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.126311 restraints weight = 6574.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.129179 restraints weight = 3945.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.131105 restraints weight = 2766.548| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3204 Z= 0.233 Angle : 0.725 11.229 4369 Z= 0.371 Chirality : 0.045 0.258 482 Planarity : 0.005 0.061 566 Dihedral : 4.912 43.536 458 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 7.23 % Allowed : 24.21 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.41), residues: 414 helix: -0.97 (1.31), residues: 15 sheet: -0.18 (0.43), residues: 146 loop : -1.73 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.001 0.001 HIS B 505 PHE 0.022 0.002 PHE B 392 TYR 0.012 0.001 TYR A 49 ARG 0.003 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8651 (mp) cc_final: 0.8120 (mt) REVERT: A 24 ARG cc_start: 0.8070 (tmm-80) cc_final: 0.7647 (ttp80) REVERT: A 79 GLN cc_start: 0.7050 (mp10) cc_final: 0.6564 (mp10) REVERT: A 82 ASP cc_start: 0.8392 (t0) cc_final: 0.8137 (t0) REVERT: C 43 LYS cc_start: 0.8598 (mmmt) cc_final: 0.8315 (ttpt) REVERT: C 59 TYR cc_start: 0.8020 (m-80) cc_final: 0.7320 (m-80) REVERT: B 351 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6904 (t80) REVERT: B 374 PHE cc_start: 0.3880 (m-10) cc_final: 0.3575 (m-80) REVERT: B 436 TRP cc_start: 0.6942 (OUTLIER) cc_final: 0.6340 (m-10) REVERT: B 505 HIS cc_start: 0.6959 (OUTLIER) cc_final: 0.6534 (m90) outliers start: 23 outliers final: 20 residues processed: 74 average time/residue: 0.1569 time to fit residues: 14.0342 Evaluate side-chains 80 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 505 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.142030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.124006 restraints weight = 6552.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.126820 restraints weight = 3978.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.128730 restraints weight = 2805.099| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 3204 Z= 0.305 Angle : 0.769 11.006 4369 Z= 0.396 Chirality : 0.046 0.271 482 Planarity : 0.005 0.065 566 Dihedral : 5.237 44.693 458 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 7.86 % Allowed : 24.53 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.40), residues: 414 helix: -1.11 (1.24), residues: 15 sheet: -0.28 (0.42), residues: 147 loop : -1.81 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 47 HIS 0.001 0.000 HIS B 505 PHE 0.020 0.002 PHE B 392 TYR 0.015 0.001 TYR A 98 ARG 0.004 0.001 ARG B 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8684 (mp) cc_final: 0.8104 (mt) REVERT: A 79 GLN cc_start: 0.7053 (mp10) cc_final: 0.6539 (mp10) REVERT: A 82 ASP cc_start: 0.8431 (t0) cc_final: 0.8182 (t0) REVERT: C 59 TYR cc_start: 0.8113 (m-80) cc_final: 0.7376 (m-80) REVERT: B 351 TYR cc_start: 0.7630 (OUTLIER) cc_final: 0.6929 (t80) REVERT: B 374 PHE cc_start: 0.4342 (m-10) cc_final: 0.3958 (m-10) REVERT: B 436 TRP cc_start: 0.7199 (OUTLIER) cc_final: 0.6623 (m-10) REVERT: B 505 HIS cc_start: 0.6970 (OUTLIER) cc_final: 0.6608 (m90) outliers start: 25 outliers final: 20 residues processed: 72 average time/residue: 0.1542 time to fit residues: 13.4901 Evaluate side-chains 78 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 505 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.144634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.126793 restraints weight = 6605.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.129636 restraints weight = 3859.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.131684 restraints weight = 2676.619| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3204 Z= 0.217 Angle : 0.717 12.061 4369 Z= 0.366 Chirality : 0.045 0.264 482 Planarity : 0.005 0.056 566 Dihedral : 4.901 42.574 458 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 7.55 % Allowed : 24.21 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.40), residues: 414 helix: -0.73 (1.38), residues: 15 sheet: -0.25 (0.42), residues: 145 loop : -1.74 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.001 0.001 HIS B 519 PHE 0.018 0.002 PHE B 392 TYR 0.011 0.001 TYR A 49 ARG 0.003 0.000 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1728.26 seconds wall clock time: 31 minutes 30.58 seconds (1890.58 seconds total)