Starting phenix.real_space_refine on Tue Feb 13 14:10:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x92_33064/02_2024/7x92_33064_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x92_33064/02_2024/7x92_33064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x92_33064/02_2024/7x92_33064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x92_33064/02_2024/7x92_33064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x92_33064/02_2024/7x92_33064_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x92_33064/02_2024/7x92_33064_trim.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 2134 2.51 5 N 557 2.21 5 O 652 1.98 5 H 3171 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 92": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6529 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "H" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1896 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1617 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.72, per 1000 atoms: 0.57 Number of scatterers: 6529 At special positions: 0 Unit cell: (69.636, 61.346, 101.967, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 O 652 8.00 N 557 7.00 C 2134 6.00 H 3171 1.00 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 5.37 Conformation dependent library (CDL) restraints added in 848.3 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 8 sheets defined 8.5% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.923A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.240A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.872A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (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 4 through 7 removed outlier: 3.712A pdb=" N THR H 69 " --> pdb=" O GLN H 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.520A pdb=" N ALA L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 33 through 38 removed outlier: 3.639A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 48 through 49 removed outlier: 3.582A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 84 hydrogen bonds defined for protein. 189 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: 2.14 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 3171 1.04 - 1.24: 413 1.24 - 1.44: 1160 1.44 - 1.63: 1853 1.63 - 1.83: 18 Bond restraints: 6615 Sorted by residual: bond pdb=" CG PRO A 507 " pdb=" CD PRO A 507 " ideal model delta sigma weight residual 1.503 1.281 0.222 3.40e-02 8.65e+02 4.25e+01 bond pdb=" N PRO A 507 " pdb=" CD PRO A 507 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.42e+00 bond pdb=" CB PRO A 507 " pdb=" CG PRO A 507 " ideal model delta sigma weight residual 1.492 1.617 -0.125 5.00e-02 4.00e+02 6.28e+00 bond pdb=" N PRO A 507 " pdb=" CA PRO A 507 " ideal model delta sigma weight residual 1.466 1.445 0.021 1.17e-02 7.31e+03 3.28e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 ... (remaining 6610 not shown) Histogram of bond angle deviations from ideal: 77.78 - 89.03: 3 89.03 - 100.28: 4 100.28 - 111.52: 6996 111.52 - 122.77: 3957 122.77 - 134.02: 885 Bond angle restraints: 11845 Sorted by residual: angle pdb=" CA PRO A 507 " pdb=" N PRO A 507 " pdb=" CD PRO A 507 " ideal model delta sigma weight residual 112.00 94.57 17.43 1.40e+00 5.10e-01 1.55e+02 angle pdb=" CB TYR L 96 " pdb=" CA TYR L 96 " pdb=" HA TYR L 96 " ideal model delta sigma weight residual 109.00 77.78 31.22 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C TYR L 96 " pdb=" CA TYR L 96 " pdb=" HA TYR L 96 " ideal model delta sigma weight residual 109.00 77.92 31.08 3.00e+00 1.11e-01 1.07e+02 angle pdb=" N TYR L 96 " pdb=" CA TYR L 96 " pdb=" HA TYR L 96 " ideal model delta sigma weight residual 110.00 82.48 27.52 3.00e+00 1.11e-01 8.41e+01 angle pdb=" N PRO A 507 " pdb=" CD PRO A 507 " pdb=" CG PRO A 507 " ideal model delta sigma weight residual 103.20 90.05 13.15 1.50e+00 4.44e-01 7.68e+01 ... (remaining 11840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 2933 21.81 - 43.63: 227 43.63 - 65.44: 54 65.44 - 87.26: 4 87.26 - 109.07: 9 Dihedral angle restraints: 3227 sinusoidal: 1718 harmonic: 1509 Sorted by residual: dihedral pdb=" C TYR L 96 " pdb=" N TYR L 96 " pdb=" CA TYR L 96 " pdb=" CB TYR L 96 " ideal model delta harmonic sigma weight residual -122.60 -145.46 22.86 0 2.50e+00 1.60e-01 8.36e+01 dihedral pdb=" N TYR L 96 " pdb=" C TYR L 96 " pdb=" CA TYR L 96 " pdb=" CB TYR L 96 " ideal model delta harmonic sigma weight residual 122.80 143.62 -20.82 0 2.50e+00 1.60e-01 6.93e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 43.61 49.39 1 1.00e+01 1.00e-02 3.35e+01 ... (remaining 3224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 506 0.183 - 0.366: 0 0.366 - 0.549: 0 0.549 - 0.732: 0 0.732 - 0.916: 1 Chirality restraints: 507 Sorted by residual: chirality pdb=" CA TYR L 96 " pdb=" N TYR L 96 " pdb=" C TYR L 96 " pdb=" CB TYR L 96 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA ILE L 39 " pdb=" N ILE L 39 " pdb=" C ILE L 39 " pdb=" CB ILE L 39 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 504 not shown) Planarity restraints: 1010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 506 " 0.100 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO A 507 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO A 507 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 507 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU L 94 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO L 95 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO L 59 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.022 5.00e-02 4.00e+02 ... (remaining 1007 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 847 2.24 - 2.83: 13998 2.83 - 3.42: 15813 3.42 - 4.01: 21902 4.01 - 4.60: 32318 Nonbonded interactions: 84878 Sorted by model distance: nonbonded pdb=" OG SER H 30 " pdb="HD21 ASN H 74 " model vdw 1.650 1.850 nonbonded pdb=" OE1 GLN L 6 " pdb=" H GLY L 101 " model vdw 1.667 1.850 nonbonded pdb=" OD1 ASN A 448 " pdb=" H ASN A 450 " model vdw 1.679 1.850 nonbonded pdb=" H TYR L 96 " pdb=" HA TYR L 96 " model vdw 1.695 1.816 nonbonded pdb=" OH TYR A 449 " pdb="HD21 ASN H 31 " model vdw 1.697 1.850 ... (remaining 84873 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 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: 0.110 Extract box with map and model: 1.180 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 26.100 Find NCS groups from input model: 0.120 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 : 0.005 0.222 3444 Z= 0.416 Angle : 0.745 17.433 4685 Z= 0.430 Chirality : 0.061 0.916 507 Planarity : 0.007 0.136 607 Dihedral : 17.172 109.073 1252 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Rotamer: Outliers : 0.27 % Allowed : 0.00 % Favored : 99.73 % Cbeta Deviations : 0.26 % 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: -2.53 (0.41), residues: 420 helix: -2.72 (1.22), residues: 20 sheet: -0.96 (0.47), residues: 143 loop : -2.10 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.001 0.000 HIS H 35 PHE 0.012 0.001 PHE A 377 TYR 0.007 0.001 TYR L 96 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 LEU cc_start: 0.8126 (pp) cc_final: 0.7842 (pp) REVERT: L 34 ASN cc_start: 0.7531 (m-40) cc_final: 0.7317 (m-40) REVERT: L 46 LEU cc_start: 0.8679 (tp) cc_final: 0.8435 (tp) outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.4372 time to fit residues: 68.7178 Evaluate side-chains 106 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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: 7.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN H 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3444 Z= 0.293 Angle : 0.652 7.562 4685 Z= 0.334 Chirality : 0.046 0.371 507 Planarity : 0.004 0.050 607 Dihedral : 11.110 74.910 512 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.48 % Favored : 84.52 % Rotamer: Outliers : 0.27 % Allowed : 4.67 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.72 (0.40), residues: 420 helix: -4.54 (0.44), residues: 24 sheet: -0.57 (0.49), residues: 128 loop : -2.30 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.001 0.001 HIS H 35 PHE 0.013 0.001 PHE A 377 TYR 0.014 0.002 TYR L 96 ARG 0.004 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 114 TYR cc_start: 0.8714 (m-80) cc_final: 0.8466 (m-10) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.3683 time to fit residues: 46.2151 Evaluate side-chains 86 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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: 2.9990 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3444 Z= 0.197 Angle : 0.607 7.826 4685 Z= 0.308 Chirality : 0.047 0.337 507 Planarity : 0.003 0.042 607 Dihedral : 8.762 54.011 512 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.81 % Favored : 85.95 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.76 (0.40), residues: 420 helix: -4.54 (0.41), residues: 24 sheet: -0.40 (0.50), residues: 124 loop : -2.42 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.001 0.001 HIS H 35 PHE 0.009 0.001 PHE A 377 TYR 0.013 0.001 TYR H 53 ARG 0.003 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3664 time to fit residues: 46.0446 Evaluate side-chains 88 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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: 6.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3444 Z= 0.205 Angle : 0.597 7.113 4685 Z= 0.306 Chirality : 0.045 0.315 507 Planarity : 0.003 0.042 607 Dihedral : 7.161 52.696 512 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.82 (0.39), residues: 420 helix: -4.57 (0.40), residues: 24 sheet: -0.59 (0.48), residues: 130 loop : -2.41 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.001 0.001 HIS H 35 PHE 0.010 0.001 PHE A 377 TYR 0.013 0.001 TYR H 53 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 LEU cc_start: 0.8159 (pp) cc_final: 0.7926 (pp) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.3422 time to fit residues: 40.1567 Evaluate side-chains 87 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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: 0.8980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3444 Z= 0.170 Angle : 0.582 7.584 4685 Z= 0.298 Chirality : 0.046 0.329 507 Planarity : 0.003 0.042 607 Dihedral : 6.660 50.073 512 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.81 % Favored : 86.19 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.82 (0.39), residues: 420 helix: -4.52 (0.41), residues: 24 sheet: -0.63 (0.48), residues: 130 loop : -2.39 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.004 0.002 HIS H 35 PHE 0.008 0.001 PHE A 377 TYR 0.011 0.001 TYR H 53 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 114 TYR cc_start: 0.8514 (m-10) cc_final: 0.8116 (m-10) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3194 time to fit residues: 39.6400 Evaluate side-chains 87 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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: 8.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3444 Z= 0.220 Angle : 0.615 8.262 4685 Z= 0.315 Chirality : 0.047 0.336 507 Planarity : 0.004 0.058 607 Dihedral : 6.502 48.408 512 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.48 % Allowed : 13.33 % Favored : 86.19 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.71 (0.40), residues: 420 helix: -3.51 (0.80), residues: 26 sheet: -0.67 (0.48), residues: 130 loop : -2.33 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP L 35 HIS 0.004 0.002 HIS H 35 PHE 0.024 0.001 PHE L 73 TYR 0.018 0.001 TYR L 36 ARG 0.010 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 114 TYR cc_start: 0.8536 (m-10) cc_final: 0.8123 (m-10) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2788 time to fit residues: 33.3022 Evaluate side-chains 85 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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: 9.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3444 Z= 0.286 Angle : 0.655 7.999 4685 Z= 0.342 Chirality : 0.046 0.312 507 Planarity : 0.004 0.042 607 Dihedral : 6.442 45.808 512 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.48 % Allowed : 15.00 % Favored : 84.52 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.87 (0.40), residues: 420 helix: -3.77 (0.69), residues: 26 sheet: -0.74 (0.48), residues: 132 loop : -2.46 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.027 0.002 PHE A 392 TYR 0.016 0.002 TYR A 489 ARG 0.007 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 49 TYR cc_start: 0.7483 (p90) cc_final: 0.7251 (p90) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2715 time to fit residues: 32.2574 Evaluate side-chains 79 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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: 10.0000 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3444 Z= 0.215 Angle : 0.600 6.414 4685 Z= 0.310 Chirality : 0.046 0.328 507 Planarity : 0.004 0.041 607 Dihedral : 6.177 42.043 512 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.48 % Allowed : 13.81 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.87 (0.39), residues: 420 helix: -3.84 (0.65), residues: 26 sheet: -0.76 (0.48), residues: 130 loop : -2.43 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.001 0.001 HIS H 35 PHE 0.023 0.002 PHE H 111 TYR 0.013 0.001 TYR A 489 ARG 0.005 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2770 time to fit residues: 32.4964 Evaluate side-chains 80 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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: 9.9990 chunk 33 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3444 Z= 0.207 Angle : 0.595 5.981 4685 Z= 0.307 Chirality : 0.046 0.342 507 Planarity : 0.003 0.042 607 Dihedral : 5.923 38.229 512 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.29 % Favored : 85.24 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.78 (0.40), residues: 420 helix: -3.76 (0.70), residues: 26 sheet: -0.86 (0.46), residues: 142 loop : -2.31 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 HIS 0.001 0.001 HIS H 35 PHE 0.017 0.002 PHE H 111 TYR 0.014 0.002 TYR L 91 ARG 0.005 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2772 time to fit residues: 33.9094 Evaluate side-chains 83 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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: 9.9990 chunk 3 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 9 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3444 Z= 0.218 Angle : 0.597 5.897 4685 Z= 0.312 Chirality : 0.046 0.353 507 Planarity : 0.004 0.042 607 Dihedral : 5.786 33.914 512 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.52 % Favored : 85.00 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.72 (0.40), residues: 420 helix: -3.70 (0.70), residues: 26 sheet: -0.87 (0.45), residues: 142 loop : -2.25 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 HIS 0.004 0.002 HIS H 35 PHE 0.031 0.002 PHE H 112 TYR 0.018 0.002 TYR L 91 ARG 0.005 0.001 ARG A 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2773 time to fit residues: 33.6952 Evaluate side-chains 81 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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: 9.9990 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.052147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.041480 restraints weight = 45559.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.044376 restraints weight = 19481.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.046392 restraints weight = 10537.608| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3444 Z= 0.178 Angle : 0.593 5.593 4685 Z= 0.309 Chirality : 0.048 0.357 507 Planarity : 0.003 0.042 607 Dihedral : 5.605 31.466 512 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.48 % Allowed : 13.57 % Favored : 85.95 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.75 (0.40), residues: 420 helix: -3.72 (0.68), residues: 26 sheet: -0.94 (0.45), residues: 142 loop : -2.22 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 47 HIS 0.004 0.002 HIS H 35 PHE 0.026 0.002 PHE H 112 TYR 0.011 0.001 TYR A 489 ARG 0.004 0.001 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2401.13 seconds wall clock time: 43 minutes 27.61 seconds (2607.61 seconds total)