Starting phenix.real_space_refine on Fri Dec 27 06:48:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpp_60351/12_2024/8zpp_60351.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpp_60351/12_2024/8zpp_60351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zpp_60351/12_2024/8zpp_60351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpp_60351/12_2024/8zpp_60351.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpp_60351/12_2024/8zpp_60351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpp_60351/12_2024/8zpp_60351.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2082 2.51 5 N 540 2.21 5 O 628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3266 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1532 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 11, 'TRANS': 180} Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 928 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Time building chain proxies: 3.41, per 1000 atoms: 1.04 Number of scatterers: 3266 At special positions: 0 Unit cell: (70.3, 68.4, 95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 628 8.00 N 540 7.00 C 2082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " 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: 0.86 Conformation dependent library (CDL) restraints added in 429.8 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 7 sheets defined 11.2% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.076A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.521A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.623A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.726A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.893A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.524A pdb=" N THR L 70 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 10.577A pdb=" N SER L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 10.555A pdb=" N SER L 68 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 10.911A pdb=" N ILE L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N SER L 66 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.525A pdb=" N MET L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR L 87 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLN L 38 " --> pdb=" O PRO L 47 " (cutoff:3.500A) 95 hydrogen bonds defined for protein. 225 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: 0.90 Time building geometry restraints manager: 1.02 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: 1022 1.34 - 1.46: 775 1.46 - 1.57: 1539 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3356 Sorted by residual: bond pdb=" CG MET L 79 " pdb=" SD MET L 79 " ideal model delta sigma weight residual 1.803 1.707 0.096 2.50e-02 1.60e+03 1.48e+01 bond pdb=" SD MET L 79 " pdb=" CE MET L 79 " ideal model delta sigma weight residual 1.791 1.697 0.094 2.50e-02 1.60e+03 1.43e+01 bond pdb=" CG LEU H 70 " pdb=" CD2 LEU H 70 " ideal model delta sigma weight residual 1.521 1.400 0.121 3.30e-02 9.18e+02 1.34e+01 bond pdb=" CA LEU H 70 " pdb=" C LEU H 70 " ideal model delta sigma weight residual 1.524 1.559 -0.035 1.23e-02 6.61e+03 8.19e+00 bond pdb=" C MET L 11 " pdb=" N ALA L 12 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.32e-02 5.74e+03 6.61e+00 ... (remaining 3351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 4251 1.28 - 2.55: 243 2.55 - 3.83: 42 3.83 - 5.11: 18 5.11 - 6.39: 8 Bond angle restraints: 4562 Sorted by residual: angle pdb=" N LEU H 70 " pdb=" CA LEU H 70 " pdb=" C LEU H 70 " ideal model delta sigma weight residual 108.73 114.63 -5.90 1.63e+00 3.76e-01 1.31e+01 angle pdb=" C VAL A 486 " pdb=" N ASN A 487 " pdb=" CA ASN A 487 " ideal model delta sigma weight residual 121.54 127.93 -6.39 1.91e+00 2.74e-01 1.12e+01 angle pdb=" C PRO H 53 " pdb=" CA PRO H 53 " pdb=" CB PRO H 53 " ideal model delta sigma weight residual 111.85 115.90 -4.05 1.42e+00 4.96e-01 8.14e+00 angle pdb=" CA TYR L 95 " pdb=" CB TYR L 95 " pdb=" CG TYR L 95 " ideal model delta sigma weight residual 113.90 109.00 4.90 1.80e+00 3.09e-01 7.43e+00 angle pdb=" C PHE A 371 " pdb=" N ALA A 372 " pdb=" CA ALA A 372 " ideal model delta sigma weight residual 123.11 118.40 4.71 1.79e+00 3.12e-01 6.93e+00 ... (remaining 4557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 1794 16.81 - 33.63: 123 33.63 - 50.44: 35 50.44 - 67.25: 4 67.25 - 84.06: 1 Dihedral angle restraints: 1957 sinusoidal: 750 harmonic: 1207 Sorted by residual: dihedral pdb=" CA GLY L 94 " pdb=" C GLY L 94 " pdb=" N TYR L 95 " pdb=" CA TYR L 95 " ideal model delta harmonic sigma weight residual -180.00 -158.22 -21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA PHE A 490 " pdb=" C PHE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta harmonic sigma weight residual -180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA LEU A 461 " pdb=" C LEU A 461 " pdb=" N LYS A 462 " pdb=" CA LYS A 462 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 409 0.069 - 0.139: 63 0.139 - 0.208: 2 0.208 - 0.278: 2 0.278 - 0.347: 2 Chirality restraints: 478 Sorted by residual: chirality pdb=" CG LEU H 70 " pdb=" CB LEU H 70 " pdb=" CD1 LEU H 70 " pdb=" CD2 LEU H 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA PRO H 53 " pdb=" N PRO H 53 " pdb=" C PRO H 53 " pdb=" CB PRO H 53 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA THR H 71 " pdb=" N THR H 71 " pdb=" C THR H 71 " pdb=" CB THR H 71 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 475 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 429 " 0.014 2.00e-02 2.50e+03 1.00e-02 1.75e+00 pdb=" CG PHE A 429 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 429 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 429 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 429 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 429 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 429 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 524 " 0.007 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C VAL A 524 " -0.022 2.00e-02 2.50e+03 pdb=" O VAL A 524 " 0.008 2.00e-02 2.50e+03 pdb=" N CYS A 525 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 95 " 0.010 2.00e-02 2.50e+03 7.59e-03 1.15e+00 pdb=" CG TYR L 95 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR L 95 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR L 95 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR L 95 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR L 95 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR L 95 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 95 " 0.001 2.00e-02 2.50e+03 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 737 2.77 - 3.30: 3078 3.30 - 3.84: 5522 3.84 - 4.37: 6617 4.37 - 4.90: 11471 Nonbonded interactions: 27425 Sorted by model distance: nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.241 3.040 nonbonded pdb=" O ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.246 3.040 nonbonded pdb=" OD2 ASP H 73 " pdb=" N SER H 76 " model vdw 2.280 3.120 nonbonded pdb=" O ILE L 29 " pdb=" OH TYR L 72 " model vdw 2.309 3.040 nonbonded pdb=" O GLY L 51 " pdb=" OG1 THR L 52 " model vdw 2.317 3.040 ... (remaining 27420 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.970 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 : 0.008 0.121 3356 Z= 0.531 Angle : 0.754 6.386 4562 Z= 0.412 Chirality : 0.052 0.347 478 Planarity : 0.004 0.032 589 Dihedral : 12.662 84.065 1179 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.42), residues: 413 helix: -3.07 (0.75), residues: 27 sheet: -0.13 (0.40), residues: 172 loop : 0.39 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.004 0.002 HIS L 35 PHE 0.022 0.002 PHE A 429 TYR 0.018 0.002 TYR L 95 ARG 0.002 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8881 (tppp) cc_final: 0.8149 (tptp) REVERT: A 455 LEU cc_start: 0.9002 (tp) cc_final: 0.8713 (tp) REVERT: A 523 THR cc_start: 0.8257 (p) cc_final: 0.7957 (p) REVERT: H 3 GLN cc_start: 0.8447 (pp30) cc_final: 0.8028 (pp30) REVERT: H 114 THR cc_start: 0.9027 (m) cc_final: 0.8514 (m) REVERT: L 104 LYS cc_start: 0.8695 (ttpp) cc_final: 0.8423 (ttpp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1882 time to fit residues: 25.3874 Evaluate side-chains 93 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN H 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3356 Z= 0.304 Angle : 0.657 5.722 4562 Z= 0.354 Chirality : 0.048 0.179 478 Planarity : 0.004 0.033 589 Dihedral : 5.498 25.689 462 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.28 % Allowed : 20.80 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.43), residues: 413 helix: -2.77 (0.86), residues: 21 sheet: -0.21 (0.41), residues: 173 loop : 0.42 (0.45), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 436 HIS 0.003 0.001 HIS A 519 PHE 0.018 0.002 PHE H 64 TYR 0.019 0.002 TYR A 365 ARG 0.003 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 CYS cc_start: 0.5281 (OUTLIER) cc_final: 0.5075 (t) REVERT: A 378 LYS cc_start: 0.8903 (tppp) cc_final: 0.8147 (tptp) REVERT: A 523 THR cc_start: 0.8140 (p) cc_final: 0.7866 (p) REVERT: H 3 GLN cc_start: 0.8265 (pp30) cc_final: 0.7672 (pp30) REVERT: H 6 GLN cc_start: 0.8333 (tt0) cc_final: 0.7985 (tt0) REVERT: H 46 GLU cc_start: 0.8122 (pt0) cc_final: 0.7836 (pt0) REVERT: H 112 GLN cc_start: 0.8346 (pm20) cc_final: 0.8032 (pm20) REVERT: H 114 THR cc_start: 0.9055 (m) cc_final: 0.8469 (m) REVERT: L 54 ASN cc_start: 0.8462 (m110) cc_final: 0.8188 (m110) REVERT: L 104 LYS cc_start: 0.8704 (ttpp) cc_final: 0.8483 (ttpp) outliers start: 8 outliers final: 5 residues processed: 107 average time/residue: 0.1908 time to fit residues: 23.9438 Evaluate side-chains 99 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 28 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.0870 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.0010 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.4564 ------------------------------------------------------------------------------- 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** H 6 GLN H 39 GLN L 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3356 Z= 0.245 Angle : 0.614 6.206 4562 Z= 0.329 Chirality : 0.047 0.146 478 Planarity : 0.004 0.037 589 Dihedral : 5.260 24.948 462 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.42 % Allowed : 22.79 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.43), residues: 413 helix: -2.45 (0.94), residues: 21 sheet: -0.22 (0.40), residues: 172 loop : 0.29 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.003 0.001 HIS A 519 PHE 0.015 0.001 PHE A 377 TYR 0.011 0.001 TYR L 95 ARG 0.004 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8956 (tppp) cc_final: 0.8219 (tptp) REVERT: A 420 ASP cc_start: 0.8394 (m-30) cc_final: 0.8062 (m-30) REVERT: A 466 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6815 (ttt180) REVERT: A 523 THR cc_start: 0.8124 (p) cc_final: 0.7844 (p) REVERT: H 3 GLN cc_start: 0.8168 (pp30) cc_final: 0.7801 (pp30) REVERT: H 34 MET cc_start: 0.7912 (tpt) cc_final: 0.7221 (tpt) REVERT: H 46 GLU cc_start: 0.8145 (pt0) cc_final: 0.7874 (pt0) REVERT: H 112 GLN cc_start: 0.8324 (pm20) cc_final: 0.8028 (pm20) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 0.1830 time to fit residues: 22.6053 Evaluate side-chains 103 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 36 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.0870 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- 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 ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3356 Z= 0.200 Angle : 0.575 6.061 4562 Z= 0.305 Chirality : 0.045 0.141 478 Planarity : 0.004 0.036 589 Dihedral : 4.973 18.579 462 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.85 % Allowed : 23.36 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.43), residues: 413 helix: -1.23 (1.50), residues: 13 sheet: -0.32 (0.39), residues: 170 loop : 0.25 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS A 519 PHE 0.013 0.001 PHE A 377 TYR 0.011 0.001 TYR H 32 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8927 (tppp) cc_final: 0.8181 (tptp) REVERT: A 420 ASP cc_start: 0.8396 (m-30) cc_final: 0.8126 (m-30) REVERT: A 523 THR cc_start: 0.8043 (p) cc_final: 0.7763 (p) REVERT: H 34 MET cc_start: 0.7943 (tpt) cc_final: 0.7235 (tpt) REVERT: H 46 GLU cc_start: 0.8190 (pt0) cc_final: 0.7921 (pt0) REVERT: H 114 THR cc_start: 0.9017 (m) cc_final: 0.8797 (p) REVERT: L 104 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8233 (ttpt) outliers start: 10 outliers final: 6 residues processed: 101 average time/residue: 0.1808 time to fit residues: 21.7077 Evaluate side-chains 103 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 76 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 493 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN H 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3356 Z= 0.282 Angle : 0.601 5.981 4562 Z= 0.316 Chirality : 0.046 0.143 478 Planarity : 0.004 0.033 589 Dihedral : 5.063 19.017 462 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.56 % Allowed : 21.94 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.43), residues: 413 helix: -1.51 (1.40), residues: 13 sheet: -0.45 (0.39), residues: 170 loop : 0.24 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 110 HIS 0.002 0.001 HIS A 519 PHE 0.011 0.001 PHE A 429 TYR 0.011 0.002 TYR A 365 ARG 0.005 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8943 (tppp) cc_final: 0.8179 (tptp) REVERT: A 420 ASP cc_start: 0.8433 (m-30) cc_final: 0.8144 (m-30) REVERT: A 466 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6730 (ttt180) REVERT: A 523 THR cc_start: 0.8192 (p) cc_final: 0.7894 (p) REVERT: H 3 GLN cc_start: 0.8111 (pp30) cc_final: 0.7659 (pp30) REVERT: H 34 MET cc_start: 0.8112 (tpt) cc_final: 0.7490 (tpt) REVERT: H 46 GLU cc_start: 0.8128 (pt0) cc_final: 0.7871 (pt0) REVERT: H 114 THR cc_start: 0.9046 (m) cc_final: 0.8769 (p) REVERT: L 54 ASN cc_start: 0.8472 (m110) cc_final: 0.8242 (m110) outliers start: 16 outliers final: 11 residues processed: 106 average time/residue: 0.1888 time to fit residues: 23.6324 Evaluate side-chains 112 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 76 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.0570 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3356 Z= 0.222 Angle : 0.589 6.032 4562 Z= 0.314 Chirality : 0.045 0.140 478 Planarity : 0.004 0.031 589 Dihedral : 4.950 18.665 462 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.99 % Allowed : 25.07 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.43), residues: 413 helix: -1.58 (1.35), residues: 13 sheet: -0.46 (0.39), residues: 170 loop : 0.27 (0.45), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 110 HIS 0.002 0.001 HIS A 519 PHE 0.009 0.001 PHE A 377 TYR 0.009 0.001 TYR A 365 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8931 (tppp) cc_final: 0.8170 (tptp) REVERT: A 462 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7853 (ttpp) REVERT: A 523 THR cc_start: 0.8126 (p) cc_final: 0.7875 (p) REVERT: H 3 GLN cc_start: 0.8061 (pp30) cc_final: 0.7628 (pp30) REVERT: H 40 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7433 (ttm-80) REVERT: H 46 GLU cc_start: 0.8172 (pt0) cc_final: 0.7960 (pt0) REVERT: L 104 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8372 (ttpt) outliers start: 14 outliers final: 9 residues processed: 110 average time/residue: 0.1892 time to fit residues: 24.5211 Evaluate side-chains 100 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 76 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** A 493 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN H 6 GLN H 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3356 Z= 0.276 Angle : 0.612 6.098 4562 Z= 0.322 Chirality : 0.046 0.145 478 Planarity : 0.004 0.030 589 Dihedral : 5.026 18.036 462 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.70 % Allowed : 25.64 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.43), residues: 413 helix: -1.67 (1.32), residues: 13 sheet: -0.51 (0.39), residues: 170 loop : 0.30 (0.45), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 353 HIS 0.002 0.001 HIS A 519 PHE 0.011 0.001 PHE A 429 TYR 0.012 0.001 TYR H 32 ARG 0.004 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 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 378 LYS cc_start: 0.8929 (tppp) cc_final: 0.8159 (tptp) REVERT: A 523 THR cc_start: 0.8275 (p) cc_final: 0.7974 (p) REVERT: H 3 GLN cc_start: 0.8139 (pp30) cc_final: 0.7689 (pp30) REVERT: L 104 LYS cc_start: 0.8658 (ttpp) cc_final: 0.8379 (ttpt) outliers start: 13 outliers final: 11 residues processed: 101 average time/residue: 0.1625 time to fit residues: 19.7375 Evaluate side-chains 105 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 76 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.0170 chunk 30 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3356 Z= 0.274 Angle : 0.631 5.960 4562 Z= 0.330 Chirality : 0.046 0.145 478 Planarity : 0.004 0.029 589 Dihedral : 5.084 17.726 462 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.70 % Allowed : 25.36 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.43), residues: 413 helix: -1.82 (1.25), residues: 13 sheet: -0.64 (0.39), residues: 170 loop : 0.21 (0.45), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 353 HIS 0.002 0.001 HIS A 519 PHE 0.010 0.001 PHE A 429 TYR 0.009 0.001 TYR H 32 ARG 0.004 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8924 (tppp) cc_final: 0.8154 (tptp) REVERT: A 457 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7857 (ttp80) REVERT: A 523 THR cc_start: 0.8303 (p) cc_final: 0.7990 (p) REVERT: H 3 GLN cc_start: 0.8105 (pp30) cc_final: 0.7660 (pp30) outliers start: 13 outliers final: 10 residues processed: 106 average time/residue: 0.1614 time to fit residues: 20.6376 Evaluate side-chains 103 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 76 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 0.0980 chunk 3 optimal weight: 0.2980 chunk 24 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 overall best weight: 0.2278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3356 Z= 0.184 Angle : 0.615 6.158 4562 Z= 0.320 Chirality : 0.046 0.139 478 Planarity : 0.004 0.031 589 Dihedral : 4.925 19.059 462 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.85 % Allowed : 25.36 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.43), residues: 413 helix: -1.91 (1.25), residues: 13 sheet: -0.57 (0.40), residues: 170 loop : 0.21 (0.45), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 353 HIS 0.002 0.001 HIS A 519 PHE 0.009 0.001 PHE A 374 TYR 0.011 0.001 TYR A 473 ARG 0.004 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8907 (tppp) cc_final: 0.8134 (tptp) REVERT: A 420 ASP cc_start: 0.8342 (m-30) cc_final: 0.8102 (m-30) REVERT: A 457 ARG cc_start: 0.8230 (ttp80) cc_final: 0.7982 (ttp80) REVERT: A 462 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7683 (ttpp) REVERT: H 3 GLN cc_start: 0.8047 (pp30) cc_final: 0.7726 (pp30) REVERT: H 46 GLU cc_start: 0.8418 (pt0) cc_final: 0.8194 (pt0) REVERT: L 104 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8170 (ttpt) outliers start: 10 outliers final: 8 residues processed: 96 average time/residue: 0.1680 time to fit residues: 19.4199 Evaluate side-chains 97 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 76 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 0.0970 chunk 29 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.0770 overall best weight: 0.3336 ------------------------------------------------------------------------------- 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** A 493 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3356 Z= 0.211 Angle : 0.614 6.078 4562 Z= 0.321 Chirality : 0.046 0.142 478 Planarity : 0.004 0.031 589 Dihedral : 4.898 18.714 462 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.85 % Allowed : 27.92 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.43), residues: 413 helix: -2.63 (1.04), residues: 13 sheet: -0.54 (0.40), residues: 170 loop : 0.18 (0.45), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.002 0.001 HIS A 519 PHE 0.021 0.001 PHE H 64 TYR 0.027 0.001 TYR A 473 ARG 0.005 0.001 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8910 (tppp) cc_final: 0.8131 (tptp) REVERT: A 420 ASP cc_start: 0.8268 (m-30) cc_final: 0.8053 (m-30) REVERT: A 462 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7760 (ttpp) REVERT: H 3 GLN cc_start: 0.8030 (pp30) cc_final: 0.7705 (pp30) REVERT: H 46 GLU cc_start: 0.8470 (pt0) cc_final: 0.8241 (pt0) REVERT: L 104 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8166 (ttpt) outliers start: 10 outliers final: 8 residues processed: 104 average time/residue: 0.1828 time to fit residues: 22.6787 Evaluate side-chains 102 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.0770 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.154065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134887 restraints weight = 4708.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138582 restraints weight = 2671.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.141117 restraints weight = 1782.230| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3356 Z= 0.252 Angle : 0.651 6.906 4562 Z= 0.339 Chirality : 0.046 0.142 478 Planarity : 0.004 0.033 589 Dihedral : 5.041 20.834 462 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.56 % Allowed : 27.92 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.43), residues: 413 helix: -2.91 (0.98), residues: 13 sheet: -0.61 (0.40), residues: 170 loop : 0.13 (0.45), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.002 0.001 HIS A 519 PHE 0.010 0.001 PHE A 429 TYR 0.024 0.002 TYR A 473 ARG 0.005 0.001 ARG A 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1462.67 seconds wall clock time: 27 minutes 35.17 seconds (1655.17 seconds total)