Starting phenix.real_space_refine on Sun Mar 10 16:28:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd2_38263/03_2024/8xd2_38263_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd2_38263/03_2024/8xd2_38263.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd2_38263/03_2024/8xd2_38263_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd2_38263/03_2024/8xd2_38263_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd2_38263/03_2024/8xd2_38263_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd2_38263/03_2024/8xd2_38263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd2_38263/03_2024/8xd2_38263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd2_38263/03_2024/8xd2_38263_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd2_38263/03_2024/8xd2_38263_neut_updated.pdb" } resolution = 2.64 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 P 3 5.49 5 S 14 5.16 5 C 2094 2.51 5 N 559 2.21 5 O 635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3305 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3255 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 50 Unusual residues: {'NAP': 1} Classifications: {'peptide': 1, 'undetermined': 1, 'water': 9} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 2.26, per 1000 atoms: 0.68 Number of scatterers: 3305 At special positions: 0 Unit cell: (69.184, 74.448, 70.688, 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 14 16.00 P 3 15.00 O 635 8.00 N 559 7.00 C 2094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 739.5 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 3 sheets defined 48.8% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 4.096A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.504A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 134 removed outlier: 5.844A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 286 removed outlier: 4.466A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 333 Processing helix chain 'A' and resid 340 through 360 removed outlier: 4.383A pdb=" N ALA A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 391 Processing helix chain 'A' and resid 395 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.729A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.152A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.609A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 165 hydrogen bonds defined for protein. 480 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: 0.91 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1064 1.34 - 1.46: 607 1.46 - 1.57: 1670 1.57 - 1.69: 2 1.69 - 1.81: 27 Bond restraints: 3370 Sorted by residual: bond pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 1.736 1.566 0.170 2.00e-02 2.50e+03 7.25e+01 bond pdb=" C4A NAP A 501 " pdb=" N3A NAP A 501 " ideal model delta sigma weight residual 1.332 1.440 -0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" C6A NAP A 501 " pdb=" N6A NAP A 501 " ideal model delta sigma weight residual 1.335 1.434 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C8A NAP A 501 " pdb=" N7A NAP A 501 " ideal model delta sigma weight residual 1.301 1.399 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C8A NAP A 501 " pdb=" N9A NAP A 501 " ideal model delta sigma weight residual 1.371 1.463 -0.092 2.00e-02 2.50e+03 2.12e+01 ... (remaining 3365 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.49: 99 106.49 - 113.41: 1856 113.41 - 120.32: 1255 120.32 - 127.23: 1317 127.23 - 134.15: 50 Bond angle restraints: 4577 Sorted by residual: angle pdb=" C ASP A 5 " pdb=" N PRO A 6 " pdb=" CA PRO A 6 " ideal model delta sigma weight residual 119.24 123.85 -4.61 1.04e+00 9.25e-01 1.97e+01 angle pdb=" N ARG A 187 " pdb=" CA ARG A 187 " pdb=" C ARG A 187 " ideal model delta sigma weight residual 112.89 118.14 -5.25 1.24e+00 6.50e-01 1.79e+01 angle pdb=" O1A NAP A 501 " pdb=" PA NAP A 501 " pdb=" O2A NAP A 501 " ideal model delta sigma weight residual 121.77 109.67 12.10 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O1N NAP A 501 " pdb=" PN NAP A 501 " pdb=" O2N NAP A 501 " ideal model delta sigma weight residual 122.51 110.57 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C PHE A 273 " pdb=" N PRO A 274 " pdb=" CA PRO A 274 " ideal model delta sigma weight residual 119.90 123.92 -4.02 1.02e+00 9.61e-01 1.55e+01 ... (remaining 4572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 1769 16.86 - 33.71: 163 33.71 - 50.57: 67 50.57 - 67.43: 23 67.43 - 84.28: 11 Dihedral angle restraints: 2033 sinusoidal: 842 harmonic: 1191 Sorted by residual: dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ASP A 48 " pdb=" CB ASP A 48 " pdb=" CG ASP A 48 " pdb=" OD1 ASP A 48 " ideal model delta sinusoidal sigma weight residual -30.00 -86.77 56.77 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CG ARG A 187 " pdb=" CD ARG A 187 " pdb=" NE ARG A 187 " pdb=" CZ ARG A 187 " ideal model delta sinusoidal sigma weight residual 180.00 -136.64 -43.36 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 2030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 396 0.059 - 0.118: 91 0.118 - 0.177: 9 0.177 - 0.236: 1 0.236 - 0.295: 1 Chirality restraints: 498 Sorted by residual: chirality pdb=" C2B NAP A 501 " pdb=" C1B NAP A 501 " pdb=" C3B NAP A 501 " pdb=" O2B NAP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.46 -0.29 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA ARG A 187 " pdb=" N ARG A 187 " pdb=" C ARG A 187 " pdb=" CB ARG A 187 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.02e-01 chirality pdb=" CA GLU A 299 " pdb=" N GLU A 299 " pdb=" C GLU A 299 " pdb=" CB GLU A 299 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 495 not shown) Planarity restraints: 583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 399 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C ALA A 399 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA A 399 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR A 400 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO A 150 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 251 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 252 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 252 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 252 " -0.025 5.00e-02 4.00e+02 ... (remaining 580 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 1429 2.94 - 3.43: 3341 3.43 - 3.92: 5752 3.92 - 4.41: 6692 4.41 - 4.90: 10825 Nonbonded interactions: 28039 Sorted by model distance: nonbonded pdb=" O1N NAP A 501 " pdb=" O2A NAP A 501 " model vdw 2.449 3.040 nonbonded pdb=" O ILE A 135 " pdb=" O HOH A 601 " model vdw 2.450 2.440 nonbonded pdb=" NH2 ARG A 58 " pdb=" OD1 ASP A 140 " model vdw 2.455 2.520 nonbonded pdb=" OH TYR A 220 " pdb=" O PRO A 257 " model vdw 2.504 2.440 nonbonded pdb=" O LYS A 229 " pdb=" OE1 GLU A 233 " model vdw 2.505 3.040 ... (remaining 28034 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 individual isotropic 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: 0.730 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: 3.510 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.880 Find NCS groups from input model: 0.090 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:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 : 0.009 0.170 3370 Z= 0.557 Angle : 0.876 12.097 4577 Z= 0.458 Chirality : 0.050 0.295 498 Planarity : 0.005 0.045 583 Dihedral : 17.617 84.283 1273 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.56 % Allowed : 3.56 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.41), residues: 414 helix: 1.47 (0.35), residues: 210 sheet: -0.55 (0.68), residues: 67 loop : -0.15 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 263 HIS 0.008 0.003 HIS A 267 PHE 0.007 0.002 PHE A 341 TYR 0.013 0.002 TYR A 363 ARG 0.007 0.001 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 263 TRP cc_start: 0.8404 (t-100) cc_final: 0.7949 (t-100) outliers start: 12 outliers final: 2 residues processed: 75 average time/residue: 1.4429 time to fit residues: 110.7248 Evaluate side-chains 50 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 222 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 0.0010 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3370 Z= 0.145 Angle : 0.484 4.939 4577 Z= 0.251 Chirality : 0.043 0.122 498 Planarity : 0.005 0.046 583 Dihedral : 10.415 56.851 498 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.89 % Allowed : 14.84 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.42), residues: 414 helix: 2.09 (0.35), residues: 210 sheet: 0.56 (0.73), residues: 60 loop : -0.24 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 263 HIS 0.006 0.002 HIS A 388 PHE 0.006 0.001 PHE A 381 TYR 0.006 0.001 TYR A 363 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 263 TRP cc_start: 0.8353 (t-100) cc_final: 0.7947 (t-100) REVERT: A 267 HIS cc_start: 0.7890 (m90) cc_final: 0.7532 (m170) REVERT: A 310 LYS cc_start: 0.8762 (mtmm) cc_final: 0.8407 (mtmm) outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 1.3188 time to fit residues: 75.9892 Evaluate side-chains 49 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 0.4980 chunk 30 optimal weight: 0.1980 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3370 Z= 0.135 Angle : 0.452 4.739 4577 Z= 0.232 Chirality : 0.042 0.123 498 Planarity : 0.004 0.044 583 Dihedral : 8.951 55.284 494 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.78 % Allowed : 16.62 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.43), residues: 414 helix: 2.28 (0.35), residues: 211 sheet: 0.46 (0.72), residues: 60 loop : -0.06 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 263 HIS 0.005 0.001 HIS A 388 PHE 0.005 0.001 PHE A 341 TYR 0.006 0.001 TYR A 250 ARG 0.002 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.372 Fit side-chains REVERT: A 263 TRP cc_start: 0.8395 (t-100) cc_final: 0.8076 (t-100) REVERT: A 310 LYS cc_start: 0.8728 (mtmm) cc_final: 0.8405 (mtmm) REVERT: A 400 TYR cc_start: 0.8860 (OUTLIER) cc_final: 0.7586 (t80) outliers start: 6 outliers final: 1 residues processed: 57 average time/residue: 1.3274 time to fit residues: 77.7437 Evaluate side-chains 52 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 400 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3370 Z= 0.136 Angle : 0.449 5.515 4577 Z= 0.228 Chirality : 0.042 0.123 498 Planarity : 0.004 0.044 583 Dihedral : 7.900 55.482 492 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.37 % Allowed : 16.32 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.43), residues: 414 helix: 2.39 (0.35), residues: 211 sheet: 0.55 (0.72), residues: 60 loop : -0.06 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 263 HIS 0.012 0.002 HIS A 267 PHE 0.006 0.001 PHE A 341 TYR 0.009 0.001 TYR A 250 ARG 0.001 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 263 TRP cc_start: 0.8421 (t-100) cc_final: 0.8042 (t-100) REVERT: A 310 LYS cc_start: 0.8688 (mtmm) cc_final: 0.8364 (mtmm) outliers start: 8 outliers final: 2 residues processed: 59 average time/residue: 1.3753 time to fit residues: 83.3197 Evaluate side-chains 53 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 395 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 0.1980 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3370 Z= 0.268 Angle : 0.513 5.869 4577 Z= 0.259 Chirality : 0.044 0.131 498 Planarity : 0.004 0.046 583 Dihedral : 7.765 54.528 492 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.48 % Allowed : 17.51 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.43), residues: 414 helix: 2.28 (0.35), residues: 210 sheet: 0.51 (0.73), residues: 60 loop : -0.08 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 355 HIS 0.007 0.002 HIS A 267 PHE 0.010 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.002 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 263 TRP cc_start: 0.8449 (t-100) cc_final: 0.8067 (t-100) REVERT: A 310 LYS cc_start: 0.8717 (mtmm) cc_final: 0.8336 (mtmm) outliers start: 5 outliers final: 2 residues processed: 54 average time/residue: 1.3792 time to fit residues: 76.5150 Evaluate side-chains 50 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 233 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3370 Z= 0.157 Angle : 0.473 5.742 4577 Z= 0.237 Chirality : 0.043 0.123 498 Planarity : 0.004 0.046 583 Dihedral : 7.373 54.430 492 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.78 % Allowed : 17.51 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.43), residues: 414 helix: 2.38 (0.35), residues: 211 sheet: 0.57 (0.73), residues: 60 loop : -0.03 (0.55), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 263 HIS 0.007 0.001 HIS A 267 PHE 0.009 0.001 PHE A 381 TYR 0.009 0.001 TYR A 250 ARG 0.004 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 263 TRP cc_start: 0.8451 (t-100) cc_final: 0.8071 (t-100) REVERT: A 310 LYS cc_start: 0.8739 (mtmm) cc_final: 0.8371 (mtmm) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 1.3570 time to fit residues: 75.3484 Evaluate side-chains 51 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 400 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS A 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 3370 Z= 0.445 Angle : 0.586 6.028 4577 Z= 0.297 Chirality : 0.048 0.155 498 Planarity : 0.005 0.048 583 Dihedral : 7.886 53.655 492 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.37 % Allowed : 16.62 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.43), residues: 414 helix: 2.07 (0.35), residues: 208 sheet: 0.34 (0.72), residues: 61 loop : -0.24 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 263 HIS 0.008 0.003 HIS A 388 PHE 0.012 0.002 PHE A 381 TYR 0.014 0.002 TYR A 363 ARG 0.004 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 263 TRP cc_start: 0.8428 (t-100) cc_final: 0.7928 (t-100) REVERT: A 299 GLU cc_start: 0.7073 (mp0) cc_final: 0.6653 (pm20) REVERT: A 310 LYS cc_start: 0.8788 (mtmm) cc_final: 0.8472 (mtmm) outliers start: 8 outliers final: 3 residues processed: 56 average time/residue: 1.3138 time to fit residues: 75.7217 Evaluate side-chains 51 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 279 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3370 Z= 0.218 Angle : 0.515 6.250 4577 Z= 0.258 Chirality : 0.044 0.123 498 Planarity : 0.004 0.048 583 Dihedral : 7.603 53.607 492 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.19 % Allowed : 18.10 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.43), residues: 414 helix: 2.24 (0.35), residues: 210 sheet: 0.31 (0.72), residues: 62 loop : -0.16 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 263 HIS 0.010 0.002 HIS A 267 PHE 0.011 0.001 PHE A 381 TYR 0.011 0.001 TYR A 250 ARG 0.004 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 263 TRP cc_start: 0.8416 (t-100) cc_final: 0.7827 (t60) REVERT: A 299 GLU cc_start: 0.6998 (mp0) cc_final: 0.6510 (pm20) REVERT: A 310 LYS cc_start: 0.8775 (mtmm) cc_final: 0.8466 (mtmm) outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 1.3525 time to fit residues: 73.7780 Evaluate side-chains 51 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 300 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3370 Z= 0.307 Angle : 0.554 6.486 4577 Z= 0.278 Chirality : 0.045 0.136 498 Planarity : 0.004 0.049 583 Dihedral : 7.615 53.315 492 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.48 % Allowed : 17.51 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.43), residues: 414 helix: 2.15 (0.35), residues: 208 sheet: 0.24 (0.72), residues: 62 loop : -0.22 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 263 HIS 0.012 0.002 HIS A 267 PHE 0.011 0.002 PHE A 341 TYR 0.012 0.002 TYR A 363 ARG 0.004 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 263 TRP cc_start: 0.8369 (t-100) cc_final: 0.7831 (t-100) REVERT: A 299 GLU cc_start: 0.7052 (mp0) cc_final: 0.6666 (pm20) REVERT: A 310 LYS cc_start: 0.8793 (mtmm) cc_final: 0.8481 (mtmm) outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 1.3685 time to fit residues: 74.5536 Evaluate side-chains 52 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 389 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.0980 chunk 3 optimal weight: 0.2980 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 29 optimal weight: 0.0570 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3370 Z= 0.132 Angle : 0.489 7.211 4577 Z= 0.243 Chirality : 0.043 0.127 498 Planarity : 0.004 0.049 583 Dihedral : 6.875 54.782 492 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.48 % Allowed : 17.51 % Favored : 81.01 % 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: 2.17 (0.43), residues: 414 helix: 2.61 (0.35), residues: 205 sheet: 0.42 (0.67), residues: 72 loop : 0.26 (0.58), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 263 HIS 0.015 0.002 HIS A 267 PHE 0.006 0.001 PHE A 381 TYR 0.010 0.001 TYR A 250 ARG 0.003 0.000 ARG A 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 263 TRP cc_start: 0.8359 (t-100) cc_final: 0.7796 (t60) REVERT: A 299 GLU cc_start: 0.6855 (mp0) cc_final: 0.6241 (pm20) REVERT: A 310 LYS cc_start: 0.8733 (mtmm) cc_final: 0.8400 (mtmm) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 1.3881 time to fit residues: 76.9742 Evaluate side-chains 51 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 0.0470 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.131356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.096295 restraints weight = 4614.913| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.84 r_work: 0.3104 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3370 Z= 0.245 Angle : 0.536 7.076 4577 Z= 0.268 Chirality : 0.044 0.127 498 Planarity : 0.004 0.049 583 Dihedral : 6.955 54.824 492 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.89 % Allowed : 18.99 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.44), residues: 414 helix: 2.33 (0.35), residues: 211 sheet: 0.41 (0.74), residues: 62 loop : -0.04 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 263 HIS 0.014 0.003 HIS A 267 PHE 0.011 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.003 0.000 ARG A 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1831.61 seconds wall clock time: 33 minutes 5.73 seconds (1985.73 seconds total)