Starting phenix.real_space_refine on Fri May 9 14:22:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c8p_16490/05_2025/8c8p_16490.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c8p_16490/05_2025/8c8p_16490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c8p_16490/05_2025/8c8p_16490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c8p_16490/05_2025/8c8p_16490.map" model { file = "/net/cci-nas-00/data/ceres_data/8c8p_16490/05_2025/8c8p_16490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c8p_16490/05_2025/8c8p_16490.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.016 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 12 5.16 5 C 1564 2.51 5 N 409 2.21 5 O 464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2449 Number of models: 1 Model: "" Number of chains: 2 Chain: "H" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 913 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Time building chain proxies: 2.27, per 1000 atoms: 0.93 Number of scatterers: 2449 At special positions: 0 Unit cell: (60.1938, 67.9967, 85.8319, 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 12 16.00 O 464 8.00 N 409 7.00 C 1564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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: 0.55 Conformation dependent library (CDL) restraints added in 295.3 milliseconds 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 566 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 6 sheets defined 13.4% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.775A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.901A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.677A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.008A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.733A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.682A pdb=" N ALA H 23 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER H 21 " --> pdb=" O THR H 7 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.420A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA H 96 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR H 114 " --> pdb=" O TYR H 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.232A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 474 57 hydrogen bonds defined for protein. 141 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: 0.54 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 785 1.34 - 1.46: 673 1.46 - 1.58: 1041 1.58 - 1.70: 0 1.70 - 1.82: 14 Bond restraints: 2513 Sorted by residual: bond pdb=" CA ILE A 410 " pdb=" CB ILE A 410 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.31e-02 5.83e+03 1.56e+00 bond pdb=" CA ASN H 76 " pdb=" CB ASN H 76 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.54e-02 4.22e+03 1.40e+00 bond pdb=" CA VAL H 118 " pdb=" CB VAL H 118 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 7.01e-01 bond pdb=" CA VAL H 48 " pdb=" CB VAL H 48 " ideal model delta sigma weight residual 1.545 1.538 0.007 9.10e-03 1.21e+04 6.61e-01 bond pdb=" N GLY A 476 " pdb=" CA GLY A 476 " ideal model delta sigma weight residual 1.458 1.451 0.007 9.20e-03 1.18e+04 6.27e-01 ... (remaining 2508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 3330 1.82 - 3.64: 71 3.64 - 5.46: 9 5.46 - 7.29: 4 7.29 - 9.11: 1 Bond angle restraints: 3415 Sorted by residual: angle pdb=" C LYS H 75 " pdb=" N ASN H 76 " pdb=" CA ASN H 76 " ideal model delta sigma weight residual 122.08 128.13 -6.05 1.47e+00 4.63e-01 1.69e+01 angle pdb=" CA LEU H 31 " pdb=" CB LEU H 31 " pdb=" CG LEU H 31 " ideal model delta sigma weight residual 116.30 125.41 -9.11 3.50e+00 8.16e-02 6.77e+00 angle pdb=" C PHE A 486 " pdb=" N ASN A 487 " pdb=" CA ASN A 487 " ideal model delta sigma weight residual 121.54 126.10 -4.56 1.91e+00 2.74e-01 5.71e+00 angle pdb=" C PHE A 497 " pdb=" N GLN A 498 " pdb=" CA GLN A 498 " ideal model delta sigma weight residual 120.97 126.69 -5.72 2.84e+00 1.24e-01 4.06e+00 angle pdb=" C SER A 371 " pdb=" N ALA A 372 " pdb=" CA ALA A 372 " ideal model delta sigma weight residual 122.40 125.31 -2.91 1.45e+00 4.76e-01 4.04e+00 ... (remaining 3410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 1317 17.44 - 34.87: 124 34.87 - 52.31: 19 52.31 - 69.75: 2 69.75 - 87.19: 2 Dihedral angle restraints: 1464 sinusoidal: 565 harmonic: 899 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 1.19 -87.19 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -117.86 31.86 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" CA GLU H 103 " pdb=" C GLU H 103 " pdb=" N LEU H 104 " pdb=" CA LEU H 104 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 1461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 220 0.034 - 0.068: 92 0.068 - 0.102: 31 0.102 - 0.135: 16 0.135 - 0.169: 4 Chirality restraints: 363 Sorted by residual: chirality pdb=" CB ILE A 472 " pdb=" CA ILE A 472 " pdb=" CG1 ILE A 472 " pdb=" CG2 ILE A 472 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA ASN H 76 " pdb=" N ASN H 76 " pdb=" C ASN H 76 " pdb=" CB ASN H 76 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB VAL H 37 " pdb=" CA VAL H 37 " pdb=" CG1 VAL H 37 " pdb=" CG2 VAL H 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 360 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO A 463 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 511 " 0.005 2.00e-02 2.50e+03 1.06e-02 1.11e+00 pdb=" C VAL A 511 " -0.018 2.00e-02 2.50e+03 pdb=" O VAL A 511 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL A 512 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO A 384 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " -0.014 5.00e-02 4.00e+02 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 654 2.79 - 3.32: 2058 3.32 - 3.85: 4163 3.85 - 4.37: 4467 4.37 - 4.90: 7751 Nonbonded interactions: 19093 Sorted by model distance: nonbonded pdb=" O GLU H 1 " pdb=" OG SER H 25 " model vdw 2.267 3.040 nonbonded pdb=" O GLY H 10 " pdb=" OG1 THR H 117 " model vdw 2.311 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.318 3.040 nonbonded pdb=" OG SER H 17 " pdb=" O MET H 82 " model vdw 2.364 3.040 nonbonded pdb=" OG SER H 17 " pdb=" OD1 ASN H 83 " model vdw 2.368 3.040 ... (remaining 19088 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=0.00 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: 1.120 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.840 Find NCS groups from input model: 0.020 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2518 Z= 0.133 Angle : 0.673 9.107 3425 Z= 0.349 Chirality : 0.048 0.169 363 Planarity : 0.004 0.031 444 Dihedral : 13.499 77.692 883 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.45), residues: 310 helix: -4.21 (0.52), residues: 34 sheet: -0.20 (0.60), residues: 74 loop : -1.37 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 519 PHE 0.008 0.001 PHE A 347 TYR 0.010 0.001 TYR A 453 ARG 0.005 0.000 ARG H 66 Details of bonding type rmsd hydrogen bonds : bond 0.27763 ( 57) hydrogen bonds : angle 12.54723 ( 141) SS BOND : bond 0.00334 ( 5) SS BOND : angle 1.37889 ( 10) covalent geometry : bond 0.00242 ( 2513) covalent geometry : angle 0.66970 ( 3415) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 20 LEU cc_start: 0.8907 (tp) cc_final: 0.8552 (tp) REVERT: H 34 MET cc_start: 0.7425 (tmm) cc_final: 0.6735 (tmm) REVERT: H 36 TRP cc_start: 0.7575 (m100) cc_final: 0.6672 (t-100) REVERT: H 78 LEU cc_start: 0.7812 (tt) cc_final: 0.7470 (tt) REVERT: A 340 GLU cc_start: 0.9163 (pt0) cc_final: 0.8881 (pm20) REVERT: A 452 LEU cc_start: 0.9286 (mm) cc_final: 0.8854 (mm) REVERT: A 454 ARG cc_start: 0.9104 (ttm-80) cc_final: 0.8809 (mtt-85) REVERT: A 465 GLU cc_start: 0.9101 (tt0) cc_final: 0.8689 (tm-30) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2446 time to fit residues: 22.9237 Evaluate side-chains 42 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.079144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.061657 restraints weight = 15507.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.063410 restraints weight = 10980.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.064588 restraints weight = 8561.021| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 2518 Z= 0.205 Angle : 0.700 9.479 3425 Z= 0.368 Chirality : 0.045 0.145 363 Planarity : 0.004 0.034 444 Dihedral : 5.049 19.919 348 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.38 % Allowed : 7.17 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.45), residues: 310 helix: -4.12 (0.46), residues: 39 sheet: -1.14 (0.49), residues: 98 loop : -0.97 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.003 0.002 HIS A 519 PHE 0.015 0.002 PHE A 347 TYR 0.015 0.001 TYR H 93 ARG 0.003 0.001 ARG A 509 Details of bonding type rmsd hydrogen bonds : bond 0.04717 ( 57) hydrogen bonds : angle 9.31346 ( 141) SS BOND : bond 0.00886 ( 5) SS BOND : angle 3.65376 ( 10) covalent geometry : bond 0.00440 ( 2513) covalent geometry : angle 0.67267 ( 3415) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.7907 (tmm) cc_final: 0.7083 (tmm) REVERT: H 36 TRP cc_start: 0.7867 (m100) cc_final: 0.7327 (t-100) REVERT: H 78 LEU cc_start: 0.8082 (tt) cc_final: 0.7475 (tt) REVERT: H 107 PHE cc_start: 0.8068 (m-10) cc_final: 0.7426 (m-80) REVERT: A 392 PHE cc_start: 0.8707 (m-80) cc_final: 0.8498 (m-10) REVERT: A 454 ARG cc_start: 0.9355 (ttm-80) cc_final: 0.8793 (mmt180) REVERT: A 461 LEU cc_start: 0.8531 (pt) cc_final: 0.7873 (pp) REVERT: A 465 GLU cc_start: 0.8958 (tt0) cc_final: 0.8112 (tm-30) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.2124 time to fit residues: 10.6666 Evaluate side-chains 33 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 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 = 0.3793 r_free = 0.3793 target = 0.081220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.064375 restraints weight = 15350.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.065962 restraints weight = 11116.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.066826 restraints weight = 8834.372| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2518 Z= 0.103 Angle : 0.570 5.186 3425 Z= 0.288 Chirality : 0.042 0.134 363 Planarity : 0.003 0.034 444 Dihedral : 4.381 22.265 348 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.46), residues: 310 helix: -3.89 (0.61), residues: 33 sheet: -0.83 (0.50), residues: 101 loop : -1.03 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 110 HIS 0.001 0.001 HIS A 519 PHE 0.006 0.001 PHE A 486 TYR 0.008 0.001 TYR H 94 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 57) hydrogen bonds : angle 8.20039 ( 141) SS BOND : bond 0.00201 ( 5) SS BOND : angle 1.74131 ( 10) covalent geometry : bond 0.00222 ( 2513) covalent geometry : angle 0.56307 ( 3415) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8095 (tmm) cc_final: 0.7416 (tmm) REVERT: H 36 TRP cc_start: 0.8029 (m100) cc_final: 0.7220 (t-100) REVERT: H 71 ARG cc_start: 0.7847 (ttp-170) cc_final: 0.7310 (ttp-170) REVERT: H 78 LEU cc_start: 0.8113 (tt) cc_final: 0.7608 (tt) REVERT: H 110 TRP cc_start: 0.8231 (m-90) cc_final: 0.7742 (m-90) REVERT: A 392 PHE cc_start: 0.8814 (m-80) cc_final: 0.8600 (m-80) REVERT: A 402 ILE cc_start: 0.9334 (tp) cc_final: 0.8969 (tp) REVERT: A 454 ARG cc_start: 0.9360 (ttm-80) cc_final: 0.9034 (mmt90) REVERT: A 461 LEU cc_start: 0.8567 (pt) cc_final: 0.8005 (pp) REVERT: A 465 GLU cc_start: 0.9053 (tt0) cc_final: 0.8303 (tm-30) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2071 time to fit residues: 11.7851 Evaluate side-chains 36 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 30 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** A 487 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 = 0.3637 r_free = 0.3637 target = 0.072313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.058326 restraints weight = 17332.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.060619 restraints weight = 15690.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.061500 restraints weight = 9692.036| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 2518 Z= 0.268 Angle : 0.771 6.904 3425 Z= 0.402 Chirality : 0.046 0.126 363 Planarity : 0.005 0.037 444 Dihedral : 5.895 24.091 348 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 24.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.44), residues: 310 helix: -3.88 (0.48), residues: 39 sheet: -0.61 (0.51), residues: 90 loop : -1.21 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 436 HIS 0.004 0.003 HIS A 519 PHE 0.031 0.002 PHE A 338 TYR 0.016 0.002 TYR H 33 ARG 0.004 0.001 ARG H 71 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 57) hydrogen bonds : angle 8.70050 ( 141) SS BOND : bond 0.00933 ( 5) SS BOND : angle 2.95945 ( 10) covalent geometry : bond 0.00564 ( 2513) covalent geometry : angle 0.75581 ( 3415) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8064 (tmm) cc_final: 0.7459 (tmm) REVERT: H 36 TRP cc_start: 0.8324 (m100) cc_final: 0.7813 (t-100) REVERT: H 72 ASP cc_start: 0.8709 (m-30) cc_final: 0.8199 (t0) REVERT: H 78 LEU cc_start: 0.8119 (tt) cc_final: 0.7708 (tt) REVERT: A 392 PHE cc_start: 0.9061 (m-80) cc_final: 0.8691 (m-80) REVERT: A 454 ARG cc_start: 0.9336 (ttm-80) cc_final: 0.8818 (mmt90) REVERT: A 461 LEU cc_start: 0.8440 (pt) cc_final: 0.8068 (pp) REVERT: A 465 GLU cc_start: 0.8883 (tt0) cc_final: 0.8337 (tm-30) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1747 time to fit residues: 8.5655 Evaluate side-chains 32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 2 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 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 = 0.3676 r_free = 0.3676 target = 0.074399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.058064 restraints weight = 17537.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.059586 restraints weight = 12660.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.060361 restraints weight = 10154.340| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 2518 Z= 0.155 Angle : 0.704 9.397 3425 Z= 0.356 Chirality : 0.047 0.312 363 Planarity : 0.004 0.042 444 Dihedral : 5.120 21.726 348 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.38 % Allowed : 3.77 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.44), residues: 310 helix: -3.33 (0.71), residues: 33 sheet: -0.03 (0.52), residues: 82 loop : -1.58 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 110 HIS 0.002 0.002 HIS A 519 PHE 0.018 0.002 PHE A 347 TYR 0.015 0.002 TYR H 33 ARG 0.003 0.001 ARG H 71 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 57) hydrogen bonds : angle 7.97543 ( 141) SS BOND : bond 0.00805 ( 5) SS BOND : angle 3.89128 ( 10) covalent geometry : bond 0.00355 ( 2513) covalent geometry : angle 0.67249 ( 3415) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8066 (tmm) cc_final: 0.7261 (tmm) REVERT: H 36 TRP cc_start: 0.8378 (m100) cc_final: 0.7525 (t-100) REVERT: H 72 ASP cc_start: 0.8727 (m-30) cc_final: 0.8237 (t0) REVERT: H 78 LEU cc_start: 0.8375 (tt) cc_final: 0.7830 (tt) REVERT: H 107 PHE cc_start: 0.7938 (m-80) cc_final: 0.7313 (m-80) REVERT: A 355 ARG cc_start: 0.9343 (ttt-90) cc_final: 0.9042 (tpp80) REVERT: A 454 ARG cc_start: 0.9427 (ttm-80) cc_final: 0.9005 (mmt90) REVERT: A 461 LEU cc_start: 0.8447 (pt) cc_final: 0.7674 (pp) REVERT: A 465 GLU cc_start: 0.8947 (tt0) cc_final: 0.8284 (tm-30) outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 0.2157 time to fit residues: 10.2688 Evaluate side-chains 32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 0.4980 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.076084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.061214 restraints weight = 16751.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.063045 restraints weight = 15106.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.064395 restraints weight = 10374.809| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 2518 Z= 0.106 Angle : 0.609 6.940 3425 Z= 0.300 Chirality : 0.044 0.146 363 Planarity : 0.003 0.035 444 Dihedral : 4.793 20.006 348 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.46), residues: 310 helix: -3.19 (0.73), residues: 33 sheet: 0.04 (0.54), residues: 83 loop : -1.44 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 110 HIS 0.002 0.001 HIS A 519 PHE 0.017 0.001 PHE A 347 TYR 0.014 0.001 TYR H 33 ARG 0.001 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.02712 ( 57) hydrogen bonds : angle 7.46603 ( 141) SS BOND : bond 0.00317 ( 5) SS BOND : angle 2.33627 ( 10) covalent geometry : bond 0.00244 ( 2513) covalent geometry : angle 0.59710 ( 3415) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.7957 (tmm) cc_final: 0.7179 (tmm) REVERT: H 36 TRP cc_start: 0.8088 (m100) cc_final: 0.7358 (t-100) REVERT: H 78 LEU cc_start: 0.8313 (tt) cc_final: 0.7742 (tt) REVERT: H 110 TRP cc_start: 0.8151 (m-90) cc_final: 0.7922 (m-90) REVERT: A 355 ARG cc_start: 0.9326 (ttt-90) cc_final: 0.9078 (tpp80) REVERT: A 454 ARG cc_start: 0.9396 (ttm-80) cc_final: 0.8947 (mmt90) REVERT: A 461 LEU cc_start: 0.8546 (pt) cc_final: 0.7874 (pp) REVERT: A 465 GLU cc_start: 0.9022 (tt0) cc_final: 0.8272 (tm-30) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.2369 time to fit residues: 10.5247 Evaluate side-chains 33 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 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 = 0.3683 r_free = 0.3683 target = 0.074603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.058867 restraints weight = 17918.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.060375 restraints weight = 12866.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.061432 restraints weight = 10207.964| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.6930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2518 Z= 0.140 Angle : 0.645 6.425 3425 Z= 0.323 Chirality : 0.044 0.155 363 Planarity : 0.003 0.032 444 Dihedral : 5.128 26.884 348 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.47), residues: 310 helix: -3.37 (0.71), residues: 33 sheet: 0.04 (0.57), residues: 84 loop : -1.36 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 36 HIS 0.002 0.001 HIS A 519 PHE 0.021 0.002 PHE A 347 TYR 0.017 0.001 TYR H 33 ARG 0.003 0.001 ARG A 509 Details of bonding type rmsd hydrogen bonds : bond 0.02968 ( 57) hydrogen bonds : angle 7.72888 ( 141) SS BOND : bond 0.00317 ( 5) SS BOND : angle 2.75845 ( 10) covalent geometry : bond 0.00311 ( 2513) covalent geometry : angle 0.62795 ( 3415) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.7963 (tmm) cc_final: 0.7297 (tmm) REVERT: H 36 TRP cc_start: 0.8085 (m100) cc_final: 0.7019 (t-100) REVERT: H 78 LEU cc_start: 0.8387 (tt) cc_final: 0.7850 (tt) REVERT: A 454 ARG cc_start: 0.9435 (ttm-80) cc_final: 0.9002 (mmt90) REVERT: A 461 LEU cc_start: 0.8540 (pt) cc_final: 0.7790 (pp) REVERT: A 465 GLU cc_start: 0.8861 (tt0) cc_final: 0.8131 (tm-30) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.2113 time to fit residues: 8.9582 Evaluate side-chains 29 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 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 = 0.3732 r_free = 0.3732 target = 0.077440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.062683 restraints weight = 16883.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.064401 restraints weight = 14298.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.065641 restraints weight = 10433.232| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.6969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2518 Z= 0.107 Angle : 0.677 12.762 3425 Z= 0.336 Chirality : 0.045 0.187 363 Planarity : 0.003 0.028 444 Dihedral : 4.907 22.493 348 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.46), residues: 310 helix: -3.33 (0.70), residues: 33 sheet: 0.20 (0.56), residues: 83 loop : -1.48 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.001 0.001 HIS A 519 PHE 0.018 0.001 PHE A 429 TYR 0.015 0.001 TYR H 33 ARG 0.002 0.000 ARG A 509 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 57) hydrogen bonds : angle 7.36841 ( 141) SS BOND : bond 0.00920 ( 5) SS BOND : angle 2.38637 ( 10) covalent geometry : bond 0.00235 ( 2513) covalent geometry : angle 0.66593 ( 3415) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.7957 (tmm) cc_final: 0.7330 (tmm) REVERT: H 36 TRP cc_start: 0.8091 (m100) cc_final: 0.7516 (t-100) REVERT: H 78 LEU cc_start: 0.8388 (tt) cc_final: 0.7954 (tt) REVERT: A 355 ARG cc_start: 0.9344 (ttt-90) cc_final: 0.9071 (tpp80) REVERT: A 402 ILE cc_start: 0.9344 (tp) cc_final: 0.9064 (tp) REVERT: A 409 GLN cc_start: 0.9655 (mt0) cc_final: 0.9404 (tt0) REVERT: A 454 ARG cc_start: 0.9399 (ttm-80) cc_final: 0.8972 (mmt90) REVERT: A 461 LEU cc_start: 0.8606 (pt) cc_final: 0.7873 (pp) REVERT: A 465 GLU cc_start: 0.8988 (tt0) cc_final: 0.8259 (tm-30) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2033 time to fit residues: 9.8321 Evaluate side-chains 32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 30 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 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 = 0.3718 r_free = 0.3718 target = 0.077067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.062111 restraints weight = 16463.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.064129 restraints weight = 11762.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.064751 restraints weight = 8541.901| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.7334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2518 Z= 0.128 Angle : 0.663 9.393 3425 Z= 0.332 Chirality : 0.045 0.165 363 Planarity : 0.003 0.028 444 Dihedral : 5.028 25.511 348 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.45), residues: 310 helix: -3.20 (0.70), residues: 33 sheet: 0.58 (0.59), residues: 73 loop : -1.46 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 110 HIS 0.002 0.001 HIS A 519 PHE 0.012 0.001 PHE A 338 TYR 0.015 0.001 TYR H 33 ARG 0.002 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02928 ( 57) hydrogen bonds : angle 7.08846 ( 141) SS BOND : bond 0.00975 ( 5) SS BOND : angle 2.61071 ( 10) covalent geometry : bond 0.00278 ( 2513) covalent geometry : angle 0.64872 ( 3415) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8065 (tmm) cc_final: 0.7459 (tmm) REVERT: H 36 TRP cc_start: 0.8438 (m100) cc_final: 0.7456 (t-100) REVERT: H 78 LEU cc_start: 0.8351 (tt) cc_final: 0.7909 (tt) REVERT: A 454 ARG cc_start: 0.9427 (ttm-80) cc_final: 0.9040 (tpp80) REVERT: A 461 LEU cc_start: 0.8630 (pt) cc_final: 0.7893 (pp) REVERT: A 465 GLU cc_start: 0.8887 (tt0) cc_final: 0.8141 (tm-30) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1936 time to fit residues: 8.6422 Evaluate side-chains 29 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 9 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 chunk 12 optimal weight: 0.0010 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 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 = 0.3741 r_free = 0.3741 target = 0.077271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.061662 restraints weight = 16704.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.063234 restraints weight = 11937.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.064329 restraints weight = 9383.166| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.7380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2518 Z= 0.097 Angle : 0.630 8.452 3425 Z= 0.310 Chirality : 0.044 0.168 363 Planarity : 0.003 0.026 444 Dihedral : 4.666 25.278 348 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.45), residues: 310 helix: -3.22 (0.68), residues: 33 sheet: 0.56 (0.57), residues: 73 loop : -1.45 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 110 HIS 0.001 0.001 HIS A 519 PHE 0.015 0.001 PHE A 429 TYR 0.016 0.001 TYR H 33 ARG 0.001 0.000 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.02956 ( 57) hydrogen bonds : angle 6.62757 ( 141) SS BOND : bond 0.00826 ( 5) SS BOND : angle 1.82856 ( 10) covalent geometry : bond 0.00213 ( 2513) covalent geometry : angle 0.62329 ( 3415) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8041 (tmm) cc_final: 0.7410 (tmm) REVERT: H 36 TRP cc_start: 0.8358 (m100) cc_final: 0.7375 (t-100) REVERT: H 78 LEU cc_start: 0.8328 (tt) cc_final: 0.7883 (tt) REVERT: A 454 ARG cc_start: 0.9396 (ttm-80) cc_final: 0.8656 (mmt180) REVERT: A 461 LEU cc_start: 0.8511 (pt) cc_final: 0.7627 (pp) REVERT: A 465 GLU cc_start: 0.8886 (tt0) cc_final: 0.8119 (tm-30) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1795 time to fit residues: 8.7914 Evaluate side-chains 31 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 23 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 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 = 0.3739 r_free = 0.3739 target = 0.076630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.061809 restraints weight = 16464.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.064483 restraints weight = 11527.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.065269 restraints weight = 7890.705| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.7596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2518 Z= 0.105 Angle : 0.642 7.901 3425 Z= 0.317 Chirality : 0.043 0.163 363 Planarity : 0.003 0.025 444 Dihedral : 4.681 25.798 348 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.45), residues: 310 helix: -3.15 (0.69), residues: 33 sheet: 0.58 (0.58), residues: 73 loop : -1.36 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 110 HIS 0.001 0.001 HIS A 519 PHE 0.014 0.001 PHE A 429 TYR 0.007 0.001 TYR A 351 ARG 0.001 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02917 ( 57) hydrogen bonds : angle 6.63184 ( 141) SS BOND : bond 0.00755 ( 5) SS BOND : angle 1.95032 ( 10) covalent geometry : bond 0.00232 ( 2513) covalent geometry : angle 0.63413 ( 3415) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1385.31 seconds wall clock time: 24 minutes 40.95 seconds (1480.95 seconds total)