Starting phenix.real_space_refine on Wed Mar 5 18:00:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cyh_30500/03_2025/7cyh_30500.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cyh_30500/03_2025/7cyh_30500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cyh_30500/03_2025/7cyh_30500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cyh_30500/03_2025/7cyh_30500.map" model { file = "/net/cci-nas-00/data/ceres_data/7cyh_30500/03_2025/7cyh_30500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cyh_30500/03_2025/7cyh_30500.cif" } resolution = 3.9 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= 0.210 sd= 1.412 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 14 5.16 5 C 2057 2.51 5 N 551 2.21 5 O 619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3241 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "D" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 806 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 899 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 2.38, per 1000 atoms: 0.73 Number of scatterers: 3241 At special positions: 0 Unit cell: (72.45, 61.95, 92.4, 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 14 16.00 O 619 8.00 N 551 7.00 C 2057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " 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: 0.75 Conformation dependent library (CDL) restraints added in 422.8 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 11 sheets defined 9.5% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.554A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.911A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.841A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.024A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 403 removed outlier: 3.650A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.885A pdb=" N CYS D 22 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 70 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 39 through 41 removed outlier: 4.021A pdb=" N VAL D 88 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.785A pdb=" N LYS E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 50 removed outlier: 6.383A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N MET E 34 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N CYS E 96 " --> pdb=" O TRP E 110 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TRP E 110 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG E 98 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 50 removed outlier: 6.383A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N MET E 34 " --> pdb=" O GLU E 50 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 156 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: 0.73 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1045 1.34 - 1.46: 891 1.46 - 1.59: 1370 1.59 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 3322 Sorted by residual: bond pdb=" C PHE A 497 " pdb=" N GLN A 498 " ideal model delta sigma weight residual 1.329 1.256 0.073 1.86e-02 2.89e+03 1.53e+01 bond pdb=" CA VAL A 512 " pdb=" C VAL A 512 " ideal model delta sigma weight residual 1.525 1.503 0.022 9.00e-03 1.23e+04 6.10e+00 bond pdb=" C GLN A 498 " pdb=" N PRO A 499 " ideal model delta sigma weight residual 1.336 1.307 0.029 1.25e-02 6.40e+03 5.50e+00 bond pdb=" CB PHE A 429 " pdb=" CG PHE A 429 " ideal model delta sigma weight residual 1.502 1.449 0.053 2.30e-02 1.89e+03 5.27e+00 bond pdb=" CB PHE A 377 " pdb=" CG PHE A 377 " ideal model delta sigma weight residual 1.502 1.449 0.053 2.30e-02 1.89e+03 5.24e+00 ... (remaining 3317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 4410 3.27 - 6.55: 95 6.55 - 9.82: 9 9.82 - 13.09: 0 13.09 - 16.36: 1 Bond angle restraints: 4515 Sorted by residual: angle pdb=" C PHE A 497 " pdb=" N GLN A 498 " pdb=" CA GLN A 498 " ideal model delta sigma weight residual 121.48 105.12 16.36 2.04e+00 2.40e-01 6.44e+01 angle pdb=" N VAL A 512 " pdb=" CA VAL A 512 " pdb=" C VAL A 512 " ideal model delta sigma weight residual 108.53 99.98 8.55 1.22e+00 6.72e-01 4.91e+01 angle pdb=" N GLY E 105 " pdb=" CA GLY E 105 " pdb=" C GLY E 105 " ideal model delta sigma weight residual 111.42 103.58 7.84 1.51e+00 4.39e-01 2.69e+01 angle pdb=" C PHE D 35 " pdb=" N MET D 36 " pdb=" CA MET D 36 " ideal model delta sigma weight residual 121.53 131.27 -9.74 2.25e+00 1.98e-01 1.87e+01 angle pdb=" C ARG D 99 " pdb=" N ILE D 100 " pdb=" CA ILE D 100 " ideal model delta sigma weight residual 121.97 128.15 -6.18 1.80e+00 3.09e-01 1.18e+01 ... (remaining 4510 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.72: 1830 15.72 - 31.43: 108 31.43 - 47.14: 7 47.14 - 62.85: 1 62.85 - 78.56: 1 Dihedral angle restraints: 1947 sinusoidal: 738 harmonic: 1209 Sorted by residual: dihedral pdb=" CA THR E 63 " pdb=" C THR E 63 " pdb=" N VAL E 64 " pdb=" CA VAL E 64 " ideal model delta harmonic sigma weight residual 180.00 146.98 33.02 0 5.00e+00 4.00e-02 4.36e+01 dihedral pdb=" CA GLN D 92 " pdb=" C GLN D 92 " pdb=" N GLN D 93 " pdb=" CA GLN D 93 " ideal model delta harmonic sigma weight residual 180.00 149.00 31.00 0 5.00e+00 4.00e-02 3.84e+01 dihedral pdb=" CA SER A 383 " pdb=" C SER A 383 " pdb=" N PRO A 384 " pdb=" CA PRO A 384 " ideal model delta harmonic sigma weight residual 180.00 -149.34 -30.66 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 1944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 263 0.042 - 0.084: 136 0.084 - 0.127: 55 0.127 - 0.169: 27 0.169 - 0.211: 3 Chirality restraints: 484 Sorted by residual: chirality pdb=" CA HIS A 519 " pdb=" N HIS A 519 " pdb=" C HIS A 519 " pdb=" CB HIS A 519 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL A 511 " pdb=" CA VAL A 511 " pdb=" CG1 VAL A 511 " pdb=" CG2 VAL A 511 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CA THR E 58 " pdb=" N THR E 58 " pdb=" C THR E 58 " pdb=" CB THR E 58 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 481 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.056 5.00e-02 4.00e+02 8.50e-02 1.16e+01 pdb=" N PRO A 527 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 398 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C ASP A 398 " 0.053 2.00e-02 2.50e+03 pdb=" O ASP A 398 " -0.020 2.00e-02 2.50e+03 pdb=" N SER A 399 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 60 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO E 61 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 61 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 61 " -0.030 5.00e-02 4.00e+02 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 107 2.65 - 3.21: 3284 3.21 - 3.77: 4889 3.77 - 4.34: 6489 4.34 - 4.90: 10557 Nonbonded interactions: 25326 Sorted by model distance: nonbonded pdb=" OG1 THR A 393 " pdb=" OE1 GLU A 516 " model vdw 2.087 3.040 nonbonded pdb=" O THR E 30 " pdb=" OG SER E 53 " model vdw 2.093 3.040 nonbonded pdb=" O SER E 52 " pdb=" NH1 ARG E 72 " model vdw 2.145 3.120 nonbonded pdb=" O LEU A 513 " pdb=" OG SER A 514 " model vdw 2.165 3.040 nonbonded pdb=" NH1 ARG A 457 " pdb=" OG SER A 459 " model vdw 2.169 3.120 ... (remaining 25321 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: 0.330 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.160 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 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 : 0.011 0.073 3322 Z= 0.702 Angle : 1.176 16.365 4515 Z= 0.656 Chirality : 0.062 0.211 484 Planarity : 0.008 0.085 589 Dihedral : 9.756 78.558 1170 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 28.64 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.83 % Favored : 89.69 % Rotamer: Outliers : 0.87 % Allowed : 0.87 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 4.76 % Twisted General : 0.75 % 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: -4.10 (0.33), residues: 417 helix: -4.58 (0.31), residues: 26 sheet: -2.91 (0.39), residues: 108 loop : -2.59 (0.31), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP A 353 HIS 0.000 0.000 HIS A 519 PHE 0.036 0.005 PHE A 497 TYR 0.032 0.004 TYR A 495 ARG 0.007 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8298 (m-80) cc_final: 0.8050 (m-80) REVERT: A 493 GLN cc_start: 0.7362 (tt0) cc_final: 0.7029 (tt0) outliers start: 3 outliers final: 3 residues processed: 112 average time/residue: 0.2154 time to fit residues: 27.6206 Evaluate side-chains 73 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 515 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.163097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.117154 restraints weight = 5307.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.119954 restraints weight = 3455.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.122124 restraints weight = 2619.622| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3322 Z= 0.252 Angle : 0.804 9.769 4515 Z= 0.419 Chirality : 0.051 0.161 484 Planarity : 0.006 0.050 589 Dihedral : 7.946 55.321 474 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.19 % Favored : 92.33 % Rotamer: Outliers : 2.62 % Allowed : 10.47 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.37), residues: 417 helix: -4.14 (0.55), residues: 25 sheet: -2.35 (0.43), residues: 104 loop : -1.61 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 353 HIS 0.001 0.001 HIS A 519 PHE 0.026 0.003 PHE A 497 TYR 0.029 0.003 TYR A 495 ARG 0.004 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.7432 (tt0) cc_final: 0.7012 (tt0) REVERT: D 56 ASN cc_start: 0.7319 (m110) cc_final: 0.6988 (m110) REVERT: E 29 PHE cc_start: 0.8850 (t80) cc_final: 0.8426 (t80) REVERT: E 34 MET cc_start: 0.7635 (mmm) cc_final: 0.7274 (mmm) REVERT: E 80 TYR cc_start: 0.8782 (m-80) cc_final: 0.8102 (m-10) outliers start: 9 outliers final: 6 residues processed: 102 average time/residue: 0.1687 time to fit residues: 20.2715 Evaluate side-chains 83 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain E residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 38 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 20.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 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 = 0.4340 r_free = 0.4340 target = 0.167238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.122959 restraints weight = 5283.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.126152 restraints weight = 3559.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.127379 restraints weight = 2480.510| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 3322 Z= 0.210 Angle : 0.794 11.512 4515 Z= 0.402 Chirality : 0.050 0.196 484 Planarity : 0.006 0.058 589 Dihedral : 7.175 56.747 473 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.24 % Favored : 93.29 % Rotamer: Outliers : 3.49 % Allowed : 13.95 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.39), residues: 417 helix: -3.96 (0.58), residues: 25 sheet: -2.04 (0.43), residues: 117 loop : -1.23 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 47 HIS 0.003 0.002 HIS A 519 PHE 0.025 0.002 PHE D 101 TYR 0.022 0.002 TYR A 495 ARG 0.007 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7806 (ttt90) cc_final: 0.7572 (ttt90) REVERT: A 406 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: D 78 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6867 (mp) REVERT: D 101 PHE cc_start: 0.8681 (m-80) cc_final: 0.8472 (m-10) REVERT: E 29 PHE cc_start: 0.8826 (t80) cc_final: 0.8239 (t80) REVERT: E 34 MET cc_start: 0.7650 (mmm) cc_final: 0.7394 (mmm) REVERT: E 47 TRP cc_start: 0.7969 (t60) cc_final: 0.7510 (t60) outliers start: 12 outliers final: 6 residues processed: 98 average time/residue: 0.1739 time to fit residues: 20.1260 Evaluate side-chains 82 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 2 optimal weight: 0.1980 chunk 14 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** D 45 GLN ** 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 = 0.4324 r_free = 0.4324 target = 0.164690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.117818 restraints weight = 5313.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.120957 restraints weight = 3364.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.123114 restraints weight = 2513.440| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3322 Z= 0.228 Angle : 0.763 11.073 4515 Z= 0.387 Chirality : 0.048 0.198 484 Planarity : 0.005 0.061 589 Dihedral : 6.777 55.845 471 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.95 % Favored : 92.57 % Rotamer: Outliers : 4.07 % Allowed : 15.70 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.40), residues: 417 helix: -3.78 (0.65), residues: 25 sheet: -1.97 (0.41), residues: 135 loop : -1.04 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 47 HIS 0.002 0.001 HIS A 519 PHE 0.015 0.002 PHE A 429 TYR 0.030 0.002 TYR D 52 ARG 0.006 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7937 (ttt90) cc_final: 0.7625 (ttt90) REVERT: A 389 ASP cc_start: 0.7499 (t70) cc_final: 0.6957 (t0) REVERT: A 506 GLN cc_start: 0.6183 (mt0) cc_final: 0.5757 (tt0) REVERT: D 37 ASN cc_start: 0.6299 (m-40) cc_final: 0.6071 (m110) REVERT: E 29 PHE cc_start: 0.8865 (t80) cc_final: 0.8242 (t80) outliers start: 14 outliers final: 10 residues processed: 90 average time/residue: 0.1557 time to fit residues: 16.8079 Evaluate side-chains 81 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.0670 chunk 34 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** D 45 GLN ** 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 = 0.4298 r_free = 0.4298 target = 0.162792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.117167 restraints weight = 5344.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.119818 restraints weight = 3575.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.121739 restraints weight = 2765.641| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3322 Z= 0.240 Angle : 0.755 11.054 4515 Z= 0.386 Chirality : 0.049 0.210 484 Planarity : 0.005 0.061 589 Dihedral : 6.450 46.779 471 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.67 % Favored : 91.85 % Rotamer: Outliers : 4.65 % Allowed : 16.57 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.41), residues: 417 helix: -3.81 (0.58), residues: 25 sheet: -1.73 (0.42), residues: 137 loop : -1.02 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 47 HIS 0.003 0.002 HIS A 519 PHE 0.019 0.002 PHE A 429 TYR 0.018 0.002 TYR D 52 ARG 0.004 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8325 (m) cc_final: 0.7779 (p) REVERT: A 355 ARG cc_start: 0.7887 (ttt90) cc_final: 0.7588 (ttt90) REVERT: A 389 ASP cc_start: 0.7332 (t70) cc_final: 0.6855 (t0) REVERT: E 29 PHE cc_start: 0.8810 (t80) cc_final: 0.8225 (t80) outliers start: 16 outliers final: 13 residues processed: 86 average time/residue: 0.1751 time to fit residues: 17.9085 Evaluate side-chains 81 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.159074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.113107 restraints weight = 5438.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.115459 restraints weight = 3895.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.115957 restraints weight = 2892.482| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3322 Z= 0.349 Angle : 0.811 11.569 4515 Z= 0.420 Chirality : 0.051 0.229 484 Planarity : 0.006 0.061 589 Dihedral : 6.474 20.640 469 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.11 % Favored : 90.41 % Rotamer: Outliers : 4.65 % Allowed : 17.44 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.41), residues: 417 helix: -4.42 (0.38), residues: 19 sheet: -1.72 (0.42), residues: 137 loop : -1.07 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 47 HIS 0.001 0.001 HIS A 519 PHE 0.024 0.003 PHE A 400 TYR 0.033 0.003 TYR D 52 ARG 0.005 0.001 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7963 (ttt90) cc_final: 0.7621 (ttt90) REVERT: A 389 ASP cc_start: 0.7299 (t70) cc_final: 0.6728 (t0) REVERT: E 83 MET cc_start: 0.6313 (tpt) cc_final: 0.5861 (tpp) outliers start: 16 outliers final: 14 residues processed: 80 average time/residue: 0.1625 time to fit residues: 15.6851 Evaluate side-chains 72 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN D 40 GLN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.162982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.116640 restraints weight = 5291.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.119476 restraints weight = 3456.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.121543 restraints weight = 2633.313| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3322 Z= 0.224 Angle : 0.752 9.308 4515 Z= 0.385 Chirality : 0.049 0.198 484 Planarity : 0.005 0.062 589 Dihedral : 6.071 21.140 469 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.43 % Favored : 91.85 % Rotamer: Outliers : 4.65 % Allowed : 17.73 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.41), residues: 417 helix: -4.31 (0.46), residues: 19 sheet: -1.61 (0.43), residues: 126 loop : -0.96 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 47 HIS 0.001 0.001 HIS A 519 PHE 0.015 0.002 PHE A 515 TYR 0.016 0.002 TYR D 52 ARG 0.008 0.001 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8479 (m) cc_final: 0.8040 (p) REVERT: A 355 ARG cc_start: 0.7877 (ttt90) cc_final: 0.7616 (tpp80) REVERT: A 389 ASP cc_start: 0.7206 (t70) cc_final: 0.6696 (t0) REVERT: E 73 ASP cc_start: 0.8409 (t0) cc_final: 0.7797 (t70) outliers start: 16 outliers final: 13 residues processed: 80 average time/residue: 0.1740 time to fit residues: 16.6775 Evaluate side-chains 75 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.0970 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN D 37 ASN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.165222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.119567 restraints weight = 5319.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.122576 restraints weight = 3437.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.124734 restraints weight = 2591.281| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3322 Z= 0.187 Angle : 0.734 8.423 4515 Z= 0.373 Chirality : 0.050 0.309 484 Planarity : 0.005 0.063 589 Dihedral : 5.704 20.198 469 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.91 % Favored : 91.37 % Rotamer: Outliers : 4.65 % Allowed : 18.02 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.42), residues: 417 helix: -4.03 (0.50), residues: 25 sheet: -1.43 (0.45), residues: 126 loop : -0.84 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 47 HIS 0.001 0.001 HIS A 519 PHE 0.014 0.002 PHE D 101 TYR 0.032 0.002 TYR D 52 ARG 0.008 0.001 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8374 (m) cc_final: 0.7984 (p) REVERT: A 355 ARG cc_start: 0.7778 (ttt90) cc_final: 0.7507 (tpp80) REVERT: A 389 ASP cc_start: 0.7096 (t70) cc_final: 0.6584 (t0) REVERT: A 465 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6754 (tm-30) outliers start: 16 outliers final: 15 residues processed: 81 average time/residue: 0.1700 time to fit residues: 16.3888 Evaluate side-chains 79 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.0270 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** D 45 GLN ** 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 = 0.4344 r_free = 0.4344 target = 0.166542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.122170 restraints weight = 5329.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.125415 restraints weight = 3314.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.127737 restraints weight = 2460.183| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.6182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3322 Z= 0.182 Angle : 0.743 7.991 4515 Z= 0.378 Chirality : 0.049 0.268 484 Planarity : 0.005 0.063 589 Dihedral : 5.560 19.784 469 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.43 % Favored : 92.09 % Rotamer: Outliers : 4.94 % Allowed : 17.73 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.42), residues: 417 helix: -3.82 (0.58), residues: 25 sheet: -1.22 (0.47), residues: 126 loop : -0.83 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 47 HIS 0.001 0.001 HIS A 519 PHE 0.016 0.002 PHE A 392 TYR 0.018 0.001 TYR E 80 ARG 0.007 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8235 (m) cc_final: 0.7816 (p) REVERT: A 392 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7942 (m-80) REVERT: A 439 ASN cc_start: 0.7589 (m-40) cc_final: 0.6954 (m-40) REVERT: A 471 GLU cc_start: 0.7278 (pp20) cc_final: 0.6873 (pt0) REVERT: E 11 LEU cc_start: 0.8007 (tp) cc_final: 0.7253 (mp) outliers start: 17 outliers final: 12 residues processed: 79 average time/residue: 0.1653 time to fit residues: 15.6386 Evaluate side-chains 74 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 20 optimal weight: 0.0370 chunk 1 optimal weight: 0.0870 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.163988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.120571 restraints weight = 5272.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.123261 restraints weight = 3728.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.124358 restraints weight = 2619.068| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3322 Z= 0.246 Angle : 0.780 8.656 4515 Z= 0.399 Chirality : 0.050 0.243 484 Planarity : 0.005 0.062 589 Dihedral : 5.783 22.523 469 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.39 % Favored : 90.89 % Rotamer: Outliers : 3.78 % Allowed : 18.31 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.43), residues: 417 helix: -3.72 (0.61), residues: 24 sheet: -1.33 (0.47), residues: 126 loop : -0.81 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP E 36 HIS 0.001 0.001 HIS A 519 PHE 0.017 0.002 PHE A 392 TYR 0.016 0.002 TYR D 52 ARG 0.007 0.001 ARG D 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8400 (m) cc_final: 0.8091 (p) REVERT: A 392 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: A 471 GLU cc_start: 0.7433 (pp20) cc_final: 0.6920 (pt0) REVERT: A 493 GLN cc_start: 0.7839 (pm20) cc_final: 0.7193 (pm20) REVERT: E 11 LEU cc_start: 0.8008 (tp) cc_final: 0.7234 (mp) REVERT: E 96 CYS cc_start: 0.4126 (p) cc_final: 0.3553 (p) outliers start: 13 outliers final: 11 residues processed: 71 average time/residue: 0.1740 time to fit residues: 14.8474 Evaluate side-chains 69 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.0040 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** 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 = 0.4286 r_free = 0.4286 target = 0.160514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.116159 restraints weight = 5393.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.118761 restraints weight = 3682.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.120499 restraints weight = 2825.397| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3322 Z= 0.308 Angle : 0.808 9.079 4515 Z= 0.414 Chirality : 0.051 0.215 484 Planarity : 0.005 0.062 589 Dihedral : 5.979 20.621 469 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.07 % Favored : 89.21 % Rotamer: Outliers : 3.78 % Allowed : 18.31 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.43), residues: 417 helix: -3.77 (0.56), residues: 18 sheet: -1.39 (0.47), residues: 124 loop : -0.94 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP E 36 HIS 0.002 0.001 HIS A 519 PHE 0.021 0.003 PHE A 392 TYR 0.017 0.002 TYR E 59 ARG 0.007 0.001 ARG D 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1549.58 seconds wall clock time: 27 minutes 39.65 seconds (1659.65 seconds total)