Starting phenix.real_space_refine on Mon Sep 23 14:34:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v27_31638/09_2024/7v27_31638.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v27_31638/09_2024/7v27_31638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v27_31638/09_2024/7v27_31638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v27_31638/09_2024/7v27_31638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v27_31638/09_2024/7v27_31638.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v27_31638/09_2024/7v27_31638.cif" } resolution = 4.18 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= 0.000 sd= 0.000 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 2065 2.51 5 N 535 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3252 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "B" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 920 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "A" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 782 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.83, per 1000 atoms: 1.18 Number of scatterers: 3252 At special positions: 0 Unit cell: (80.542, 58.576, 99.37, 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 636 8.00 N 535 7.00 C 2065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 90 " 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 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 483.1 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 10 sheets defined 5.5% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.892A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.642A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'B' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 357 removed outlier: 3.604A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 379 through 380 removed outlier: 4.202A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 removed outlier: 4.024A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.680A pdb=" N ARG B 5 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.717A pdb=" N VAL B 12 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 114 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B 36 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU B 52 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TRP B 38 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 60 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.717A pdb=" N VAL B 12 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 114 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'A' and resid 19 through 22 removed outlier: 3.639A pdb=" N SER A 67 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.028A pdb=" N LEU A 48 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLN A 39 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 50 " --> pdb=" O TRP A 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.028A pdb=" N LEU A 48 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLN A 39 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 50 " --> pdb=" O TRP A 37 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 88 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 104 " --> pdb=" O TYR A 88 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 171 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: 0.85 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1026 1.35 - 1.47: 885 1.47 - 1.59: 1403 1.59 - 1.71: 0 1.71 - 1.83: 19 Bond restraints: 3333 Sorted by residual: bond pdb=" C VAL C 382 " pdb=" N SER C 383 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.37e-02 5.33e+03 2.96e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" C5 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.14e+00 bond pdb=" C3 NAG C 601 " pdb=" O3 NAG C 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" N CYS C 391 " pdb=" CA CYS C 391 " ideal model delta sigma weight residual 1.455 1.465 -0.010 1.21e-02 6.83e+03 6.90e-01 ... (remaining 3328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 4149 0.83 - 1.67: 303 1.67 - 2.50: 51 2.50 - 3.34: 36 3.34 - 4.17: 5 Bond angle restraints: 4544 Sorted by residual: angle pdb=" N MET A 49 " pdb=" CA MET A 49 " pdb=" C MET A 49 " ideal model delta sigma weight residual 114.04 110.56 3.48 1.24e+00 6.50e-01 7.89e+00 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 107.88 111.39 -3.51 1.41e+00 5.03e-01 6.18e+00 angle pdb=" N SER A 97 " pdb=" CA SER A 97 " pdb=" C SER A 97 " ideal model delta sigma weight residual 108.34 111.47 -3.13 1.31e+00 5.83e-01 5.70e+00 angle pdb=" CA GLY C 504 " pdb=" C GLY C 504 " pdb=" N TYR C 505 " ideal model delta sigma weight residual 118.95 116.79 2.16 1.06e+00 8.90e-01 4.17e+00 angle pdb=" C PHE C 486 " pdb=" N ASN C 487 " pdb=" CA ASN C 487 " ideal model delta sigma weight residual 121.54 125.16 -3.62 1.91e+00 2.74e-01 3.60e+00 ... (remaining 4539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.03: 1763 15.03 - 30.06: 183 30.06 - 45.10: 30 45.10 - 60.13: 6 60.13 - 75.16: 1 Dihedral angle restraints: 1983 sinusoidal: 765 harmonic: 1218 Sorted by residual: dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 53.66 39.34 1 1.00e+01 1.00e-02 2.18e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 97 " pdb=" CB CYS B 97 " ideal model delta sinusoidal sigma weight residual 93.00 123.94 -30.94 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual -86.00 -58.76 -27.24 1 1.00e+01 1.00e-02 1.06e+01 ... (remaining 1980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 364 0.038 - 0.075: 103 0.075 - 0.113: 38 0.113 - 0.150: 5 0.150 - 0.188: 1 Chirality restraints: 511 Sorted by residual: chirality pdb=" CB ILE C 410 " pdb=" CA ILE C 410 " pdb=" CG1 ILE C 410 " pdb=" CG2 ILE C 410 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CB THR C 500 " pdb=" CA THR C 500 " pdb=" OG1 THR C 500 " pdb=" CG2 THR C 500 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA ILE B 39 " pdb=" N ILE B 39 " pdb=" C ILE B 39 " pdb=" CB ILE B 39 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 508 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.016 5.00e-02 4.00e+02 2.43e-02 9.46e-01 pdb=" N PRO C 521 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 45 " -0.015 5.00e-02 4.00e+02 2.26e-02 8.18e-01 pdb=" N PRO A 46 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 46 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 46 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 31 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.03e-01 pdb=" N PRO B 32 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " 0.012 5.00e-02 4.00e+02 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 546 2.76 - 3.30: 3043 3.30 - 3.83: 5332 3.83 - 4.37: 5987 4.37 - 4.90: 10409 Nonbonded interactions: 25317 Sorted by model distance: nonbonded pdb=" OG1 THR C 430 " pdb=" O PHE C 515 " model vdw 2.229 3.040 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.252 3.040 nonbonded pdb=" O ILE B 106 " pdb=" OH TYR A 38 " model vdw 2.272 3.040 nonbonded pdb=" OG SER A 9 " pdb=" O LYS A 105 " model vdw 2.309 3.040 nonbonded pdb=" O ARG C 408 " pdb=" NE2 GLN C 414 " model vdw 2.313 3.120 ... (remaining 25312 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: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.190 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 0.027 3333 Z= 0.138 Angle : 0.535 4.173 4544 Z= 0.306 Chirality : 0.040 0.188 511 Planarity : 0.003 0.024 580 Dihedral : 11.752 75.160 1191 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % 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: -4.40 (0.34), residues: 415 helix: -3.86 (0.99), residues: 13 sheet: -2.42 (0.44), residues: 126 loop : -3.32 (0.29), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 55 HIS 0.001 0.000 HIS A 41 PHE 0.008 0.001 PHE C 338 TYR 0.007 0.001 TYR B 96 ARG 0.001 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 358 ILE cc_start: 0.9209 (mm) cc_final: 0.8991 (mt) REVERT: C 365 TYR cc_start: 0.8446 (m-80) cc_final: 0.8231 (m-80) REVERT: C 405 ASP cc_start: 0.9094 (m-30) cc_final: 0.8536 (m-30) REVERT: C 408 ARG cc_start: 0.8609 (ptt90) cc_final: 0.8409 (ptt90) REVERT: C 449 TYR cc_start: 0.8758 (m-80) cc_final: 0.8529 (m-10) REVERT: C 458 LYS cc_start: 0.8492 (pptt) cc_final: 0.8042 (pttm) REVERT: B 13 LYS cc_start: 0.7872 (mmtm) cc_final: 0.7520 (tmtt) REVERT: B 49 TRP cc_start: 0.8957 (t60) cc_final: 0.8684 (t60) REVERT: B 56 ASP cc_start: 0.8641 (m-30) cc_final: 0.8436 (m-30) REVERT: B 104 ASP cc_start: 0.8474 (t0) cc_final: 0.8220 (t0) REVERT: A 64 PHE cc_start: 0.8558 (m-80) cc_final: 0.8332 (m-10) REVERT: A 68 LYS cc_start: 0.7546 (tmmt) cc_final: 0.7346 (ptmt) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2267 time to fit residues: 28.9658 Evaluate side-chains 67 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 0.0570 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 20 optimal weight: 0.0370 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN C 448 ASN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 HIS A 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3333 Z= 0.224 Angle : 0.602 6.001 4544 Z= 0.310 Chirality : 0.045 0.196 511 Planarity : 0.004 0.026 580 Dihedral : 4.645 38.583 480 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.36), residues: 415 helix: -3.66 (0.90), residues: 13 sheet: -2.08 (0.45), residues: 125 loop : -2.80 (0.32), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.000 0.000 HIS A 41 PHE 0.011 0.001 PHE C 392 TYR 0.014 0.002 TYR C 421 ARG 0.003 0.001 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 364 ASP cc_start: 0.8015 (p0) cc_final: 0.7651 (p0) REVERT: C 398 ASP cc_start: 0.9131 (m-30) cc_final: 0.8685 (m-30) REVERT: C 458 LYS cc_start: 0.8691 (pptt) cc_final: 0.8295 (pttm) REVERT: B 13 LYS cc_start: 0.7924 (mmtm) cc_final: 0.7596 (tmtt) REVERT: B 40 ARG cc_start: 0.8833 (ptt180) cc_final: 0.8071 (ptt180) REVERT: B 45 LYS cc_start: 0.9251 (tptp) cc_final: 0.9025 (tptp) REVERT: B 49 TRP cc_start: 0.8801 (t60) cc_final: 0.8412 (t60) REVERT: B 56 ASP cc_start: 0.8771 (m-30) cc_final: 0.8552 (m-30) REVERT: B 57 ASP cc_start: 0.8603 (t0) cc_final: 0.8386 (t0) REVERT: B 104 ASP cc_start: 0.8668 (t0) cc_final: 0.8436 (t0) REVERT: A 64 PHE cc_start: 0.8238 (m-80) cc_final: 0.7447 (m-10) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1951 time to fit residues: 19.4747 Evaluate side-chains 65 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 ASN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3333 Z= 0.245 Angle : 0.595 8.031 4544 Z= 0.305 Chirality : 0.044 0.195 511 Planarity : 0.004 0.026 580 Dihedral : 4.847 40.909 480 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % 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: -3.35 (0.37), residues: 415 helix: -3.15 (1.10), residues: 13 sheet: -1.85 (0.45), residues: 125 loop : -2.49 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 55 HIS 0.002 0.001 HIS A 41 PHE 0.010 0.001 PHE C 392 TYR 0.025 0.002 TYR C 495 ARG 0.003 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 364 ASP cc_start: 0.7808 (p0) cc_final: 0.7491 (p0) REVERT: C 390 LEU cc_start: 0.8650 (tp) cc_final: 0.8381 (tp) REVERT: C 394 ASN cc_start: 0.7622 (t0) cc_final: 0.6810 (t0) REVERT: C 398 ASP cc_start: 0.9113 (m-30) cc_final: 0.8679 (m-30) REVERT: C 405 ASP cc_start: 0.9132 (m-30) cc_final: 0.8739 (m-30) REVERT: C 458 LYS cc_start: 0.8717 (pptt) cc_final: 0.8253 (pttm) REVERT: B 13 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7791 (tmtt) REVERT: B 49 TRP cc_start: 0.8952 (t60) cc_final: 0.8613 (t60) REVERT: A 55 LYS cc_start: 0.8830 (mtmm) cc_final: 0.8323 (mtmm) REVERT: A 75 LEU cc_start: 0.8842 (tt) cc_final: 0.8628 (tt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1733 time to fit residues: 17.0033 Evaluate side-chains 65 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3333 Z= 0.237 Angle : 0.609 7.871 4544 Z= 0.309 Chirality : 0.044 0.194 511 Planarity : 0.004 0.029 580 Dihedral : 4.896 40.592 480 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: -3.15 (0.38), residues: 415 helix: -3.11 (1.05), residues: 13 sheet: -1.70 (0.47), residues: 125 loop : -2.36 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 55 HIS 0.001 0.000 HIS A 41 PHE 0.014 0.002 PHE C 338 TYR 0.013 0.002 TYR A 93 ARG 0.008 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 390 LEU cc_start: 0.8714 (tp) cc_final: 0.8496 (tp) REVERT: C 394 ASN cc_start: 0.7365 (t0) cc_final: 0.6478 (t0) REVERT: C 398 ASP cc_start: 0.9132 (m-30) cc_final: 0.8635 (m-30) REVERT: C 405 ASP cc_start: 0.8921 (m-30) cc_final: 0.8403 (m-30) REVERT: C 408 ARG cc_start: 0.8538 (pmt170) cc_final: 0.7814 (pmt170) REVERT: B 13 LYS cc_start: 0.8066 (mmtm) cc_final: 0.7804 (tmtt) REVERT: B 49 TRP cc_start: 0.8922 (t60) cc_final: 0.8453 (t60) REVERT: B 57 ASP cc_start: 0.8568 (t0) cc_final: 0.8362 (t0) REVERT: A 49 MET cc_start: 0.7937 (ttm) cc_final: 0.7449 (ttm) REVERT: A 64 PHE cc_start: 0.8093 (m-80) cc_final: 0.7639 (m-10) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1986 time to fit residues: 19.2389 Evaluate side-chains 63 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.0030 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.0030 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 overall best weight: 0.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 493 GLN A 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3333 Z= 0.199 Angle : 0.592 6.582 4544 Z= 0.301 Chirality : 0.044 0.220 511 Planarity : 0.004 0.047 580 Dihedral : 4.797 38.917 480 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -2.97 (0.38), residues: 415 helix: -3.05 (1.05), residues: 13 sheet: -1.60 (0.46), residues: 130 loop : -2.20 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 55 HIS 0.000 0.000 HIS A 41 PHE 0.007 0.001 PHE C 392 TYR 0.022 0.002 TYR C 495 ARG 0.007 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 364 ASP cc_start: 0.8129 (p0) cc_final: 0.7731 (p0) REVERT: C 390 LEU cc_start: 0.8657 (tp) cc_final: 0.8360 (tp) REVERT: C 394 ASN cc_start: 0.7555 (t0) cc_final: 0.6724 (t0) REVERT: C 398 ASP cc_start: 0.9025 (m-30) cc_final: 0.8512 (m-30) REVERT: C 405 ASP cc_start: 0.8930 (m-30) cc_final: 0.8519 (m-30) REVERT: C 408 ARG cc_start: 0.8506 (pmt170) cc_final: 0.7774 (pmt170) REVERT: B 13 LYS cc_start: 0.8079 (mmtm) cc_final: 0.7804 (tmtt) REVERT: B 49 TRP cc_start: 0.8826 (t60) cc_final: 0.8261 (t60) REVERT: B 57 ASP cc_start: 0.8571 (t0) cc_final: 0.8352 (t0) REVERT: A 49 MET cc_start: 0.7920 (ttm) cc_final: 0.7480 (ttm) REVERT: A 64 PHE cc_start: 0.8000 (m-80) cc_final: 0.7610 (m-10) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1610 time to fit residues: 15.0793 Evaluate side-chains 62 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3333 Z= 0.247 Angle : 0.631 7.181 4544 Z= 0.322 Chirality : 0.045 0.234 511 Planarity : 0.004 0.035 580 Dihedral : 5.041 41.919 480 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: -2.79 (0.39), residues: 415 helix: -2.86 (1.03), residues: 13 sheet: -1.56 (0.47), residues: 130 loop : -2.03 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 55 HIS 0.000 0.000 HIS A 41 PHE 0.012 0.001 PHE C 338 TYR 0.013 0.002 TYR A 93 ARG 0.006 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 364 ASP cc_start: 0.8202 (p0) cc_final: 0.7859 (p0) REVERT: C 390 LEU cc_start: 0.8686 (tp) cc_final: 0.8389 (tp) REVERT: C 398 ASP cc_start: 0.9002 (m-30) cc_final: 0.8521 (m-30) REVERT: B 49 TRP cc_start: 0.8955 (t60) cc_final: 0.8418 (t60) REVERT: B 57 ASP cc_start: 0.8633 (t0) cc_final: 0.8426 (t0) REVERT: B 59 LYS cc_start: 0.9057 (mptt) cc_final: 0.8487 (mptt) REVERT: B 71 ILE cc_start: 0.9390 (tp) cc_final: 0.8901 (tp) REVERT: A 49 MET cc_start: 0.8121 (ttm) cc_final: 0.7680 (ttm) REVERT: A 64 PHE cc_start: 0.8086 (m-80) cc_final: 0.7525 (m-10) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1776 time to fit residues: 16.4969 Evaluate side-chains 61 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.0670 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3333 Z= 0.221 Angle : 0.632 6.347 4544 Z= 0.325 Chirality : 0.046 0.253 511 Planarity : 0.004 0.056 580 Dihedral : 5.023 40.067 480 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer: Outliers : 0.28 % Allowed : 1.67 % Favored : 98.06 % 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: -2.67 (0.39), residues: 415 helix: -2.78 (0.99), residues: 13 sheet: -1.53 (0.47), residues: 130 loop : -1.92 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 37 HIS 0.000 0.000 HIS C 519 PHE 0.007 0.001 PHE C 342 TYR 0.017 0.002 TYR C 495 ARG 0.009 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 377 PHE cc_start: 0.9250 (t80) cc_final: 0.8903 (t80) REVERT: C 390 LEU cc_start: 0.8690 (tp) cc_final: 0.8303 (tp) REVERT: C 394 ASN cc_start: 0.7542 (t0) cc_final: 0.6693 (t0) REVERT: C 398 ASP cc_start: 0.8957 (m-30) cc_final: 0.8471 (m-30) REVERT: B 13 LYS cc_start: 0.8058 (mmtm) cc_final: 0.7804 (tmtt) REVERT: B 20 LEU cc_start: 0.9215 (tp) cc_final: 0.9014 (tp) REVERT: B 49 TRP cc_start: 0.8939 (t60) cc_final: 0.8171 (t60) REVERT: A 49 MET cc_start: 0.8122 (ttm) cc_final: 0.7712 (ttm) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.1700 time to fit residues: 16.2335 Evaluate side-chains 59 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.0370 chunk 35 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 overall best weight: 0.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3333 Z= 0.182 Angle : 0.645 6.610 4544 Z= 0.329 Chirality : 0.046 0.263 511 Planarity : 0.004 0.045 580 Dihedral : 4.817 37.719 480 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: -2.45 (0.40), residues: 415 helix: -2.16 (1.18), residues: 13 sheet: -1.31 (0.47), residues: 126 loop : -1.84 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 37 HIS 0.001 0.000 HIS A 41 PHE 0.009 0.001 PHE C 392 TYR 0.016 0.001 TYR A 93 ARG 0.009 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 364 ASP cc_start: 0.8258 (p0) cc_final: 0.7859 (p0) REVERT: C 377 PHE cc_start: 0.9132 (t80) cc_final: 0.8690 (t80) REVERT: C 394 ASN cc_start: 0.7446 (t0) cc_final: 0.6532 (t0) REVERT: C 398 ASP cc_start: 0.8901 (m-30) cc_final: 0.8482 (m-30) REVERT: B 13 LYS cc_start: 0.8098 (mmtm) cc_final: 0.7830 (tmtt) REVERT: B 49 TRP cc_start: 0.8865 (t60) cc_final: 0.8160 (t60) REVERT: A 55 LYS cc_start: 0.8684 (mtmm) cc_final: 0.8057 (mtmm) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1945 time to fit residues: 18.2237 Evaluate side-chains 62 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3333 Z= 0.227 Angle : 0.658 6.624 4544 Z= 0.335 Chirality : 0.046 0.274 511 Planarity : 0.004 0.041 580 Dihedral : 4.996 38.826 480 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: -2.35 (0.39), residues: 415 helix: -2.07 (1.15), residues: 13 sheet: -1.26 (0.48), residues: 117 loop : -1.75 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 37 HIS 0.001 0.000 HIS A 41 PHE 0.014 0.001 PHE C 497 TYR 0.017 0.002 TYR C 495 ARG 0.007 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 364 ASP cc_start: 0.8262 (p0) cc_final: 0.7869 (p0) REVERT: C 377 PHE cc_start: 0.9182 (t80) cc_final: 0.8840 (t80) REVERT: C 394 ASN cc_start: 0.7607 (t0) cc_final: 0.6757 (t0) REVERT: C 398 ASP cc_start: 0.8909 (m-30) cc_final: 0.8444 (m-30) REVERT: B 13 LYS cc_start: 0.8098 (mmtm) cc_final: 0.7630 (tmtt) REVERT: B 49 TRP cc_start: 0.8840 (t60) cc_final: 0.8129 (t60) REVERT: B 87 MET cc_start: 0.7576 (ttm) cc_final: 0.7244 (ttp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1941 time to fit residues: 17.1238 Evaluate side-chains 55 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3333 Z= 0.299 Angle : 0.699 6.682 4544 Z= 0.362 Chirality : 0.047 0.250 511 Planarity : 0.005 0.038 580 Dihedral : 5.485 42.214 480 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: -2.36 (0.39), residues: 415 helix: -0.94 (1.85), residues: 7 sheet: -1.28 (0.46), residues: 120 loop : -1.80 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 37 HIS 0.001 0.001 HIS C 519 PHE 0.024 0.002 PHE C 497 TYR 0.021 0.002 TYR A 32 ARG 0.005 0.001 ARG A 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 394 ASN cc_start: 0.7078 (t0) cc_final: 0.6142 (t0) REVERT: C 398 ASP cc_start: 0.8935 (m-30) cc_final: 0.8422 (m-30) REVERT: C 408 ARG cc_start: 0.8823 (pmt-80) cc_final: 0.8460 (pmt-80) REVERT: C 414 GLN cc_start: 0.7579 (pm20) cc_final: 0.7346 (pm20) REVERT: B 49 TRP cc_start: 0.9011 (t60) cc_final: 0.8393 (t60) REVERT: B 87 MET cc_start: 0.7808 (ttm) cc_final: 0.7354 (ttp) REVERT: B 100 LEU cc_start: 0.9149 (tp) cc_final: 0.8866 (tt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1808 time to fit residues: 16.9094 Evaluate side-chains 60 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 16 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.067897 restraints weight = 11825.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.070443 restraints weight = 7047.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.072199 restraints weight = 4851.028| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3333 Z= 0.260 Angle : 0.684 6.692 4544 Z= 0.355 Chirality : 0.046 0.268 511 Planarity : 0.004 0.039 580 Dihedral : 5.407 41.149 480 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -2.36 (0.39), residues: 415 helix: -0.25 (2.05), residues: 7 sheet: -1.46 (0.45), residues: 121 loop : -1.73 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 37 HIS 0.000 0.000 HIS C 519 PHE 0.020 0.002 PHE C 497 TYR 0.010 0.002 TYR C 453 ARG 0.004 0.001 ARG C 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1418.24 seconds wall clock time: 25 minutes 58.80 seconds (1558.80 seconds total)