Starting phenix.real_space_refine on Thu Dec 7 16:47:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/12_2023/7cah_30331.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/12_2023/7cah_30331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/12_2023/7cah_30331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/12_2023/7cah_30331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/12_2023/7cah_30331.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/12_2023/7cah_30331.pdb" } resolution = 3.9 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= 0.212 sd= 3.720 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 1842 2.51 5 N 473 2.21 5 O 567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2889 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 704 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "E" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1282 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 105 Time building chain proxies: 2.15, per 1000 atoms: 0.74 Number of scatterers: 2889 At special positions: 0 Unit cell: (68.64, 72.8, 64.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 7 16.00 O 567 8.00 N 473 7.00 C 1842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 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: 1.10 Conformation dependent library (CDL) restraints added in 620.3 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 7 sheets defined 11.9% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.717A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.618A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.741A pdb=" N VAL D 12 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 18 through 22 Processing sheet with id=AA3, first strand: chain 'D' and resid 52 through 53 removed outlier: 5.155A pdb=" N SER D 42 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS D 38 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TRP D 34 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.748A pdb=" N LYS E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TRP E 47 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 96 hydrogen bonds defined for protein. 213 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: 0.71 Time building geometry restraints manager: 1.20 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: 923 1.34 - 1.46: 741 1.46 - 1.58: 1294 1.58 - 1.70: 0 1.70 - 1.82: 7 Bond restraints: 2965 Sorted by residual: bond pdb=" C ILE E 51 " pdb=" N ASP E 52 " ideal model delta sigma weight residual 1.330 1.269 0.061 1.47e-02 4.63e+03 1.73e+01 bond pdb=" C ASP E 102 " pdb=" N PRO E 103 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.11e+00 bond pdb=" C THR A 430 " pdb=" N GLY A 431 " ideal model delta sigma weight residual 1.328 1.338 -0.010 1.13e-02 7.83e+03 8.60e-01 bond pdb=" N CYS A 379 " pdb=" CA CYS A 379 " ideal model delta sigma weight residual 1.458 1.447 0.011 1.19e-02 7.06e+03 8.56e-01 bond pdb=" CB TRP D 93 " pdb=" CG TRP D 93 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 8.43e-01 ... (remaining 2960 not shown) Histogram of bond angle deviations from ideal: 102.35 - 109.77: 448 109.77 - 117.19: 1658 117.19 - 124.60: 1897 124.60 - 132.02: 53 132.02 - 139.44: 8 Bond angle restraints: 4064 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 123.14 -8.74 2.30e+00 1.89e-01 1.44e+01 angle pdb=" C LYS A 378 " pdb=" N CYS A 379 " pdb=" CA CYS A 379 " ideal model delta sigma weight residual 123.00 118.23 4.77 1.41e+00 5.03e-01 1.14e+01 angle pdb=" C LYS E 12 " pdb=" N LYS E 13 " pdb=" CA LYS E 13 " ideal model delta sigma weight residual 120.81 139.44 -18.63 5.77e+00 3.00e-02 1.04e+01 angle pdb=" C ILE E 51 " pdb=" N ASP E 52 " pdb=" CA ASP E 52 " ideal model delta sigma weight residual 120.68 115.86 4.82 1.52e+00 4.33e-01 1.00e+01 angle pdb=" N HIS A 519 " pdb=" CA HIS A 519 " pdb=" C HIS A 519 " ideal model delta sigma weight residual 114.09 109.34 4.75 1.55e+00 4.16e-01 9.40e+00 ... (remaining 4059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 1503 15.51 - 31.02: 170 31.02 - 46.53: 33 46.53 - 62.04: 1 62.04 - 77.55: 3 Dihedral angle restraints: 1710 sinusoidal: 535 harmonic: 1175 Sorted by residual: dihedral pdb=" CA ASP E 102 " pdb=" C ASP E 102 " pdb=" N PRO E 103 " pdb=" CA PRO E 103 " ideal model delta harmonic sigma weight residual -180.00 -137.55 -42.45 0 5.00e+00 4.00e-02 7.21e+01 dihedral pdb=" CA CYS A 432 " pdb=" C CYS A 432 " pdb=" N VAL A 433 " pdb=" CA VAL A 433 " ideal model delta harmonic sigma weight residual -180.00 -149.72 -30.28 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 149.85 30.15 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 1707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 259 0.033 - 0.065: 116 0.065 - 0.098: 48 0.098 - 0.131: 23 0.131 - 0.163: 7 Chirality restraints: 453 Sorted by residual: chirality pdb=" CA CYS A 432 " pdb=" N CYS A 432 " pdb=" C CYS A 432 " pdb=" CB CYS A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA VAL D 12 " pdb=" N VAL D 12 " pdb=" C VAL D 12 " pdb=" CB VAL D 12 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 450 not shown) Planarity restraints: 531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 102 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO E 103 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 411 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO A 412 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO A 521 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.023 5.00e-02 4.00e+02 ... (remaining 528 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 127 2.69 - 3.24: 3052 3.24 - 3.79: 4383 3.79 - 4.35: 5694 4.35 - 4.90: 9144 Nonbonded interactions: 22400 Sorted by model distance: nonbonded pdb=" OG SER E 119 " pdb=" O ALA E 121 " model vdw 2.137 2.440 nonbonded pdb=" O ASP E 102 " pdb=" N TYR E 104 " model vdw 2.222 2.520 nonbonded pdb=" OD2 ASP E 60 " pdb=" NZ LYS E 65 " model vdw 2.242 2.520 nonbonded pdb=" OD1 ASN A 437 " pdb=" N SER A 438 " model vdw 2.297 2.520 nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.336 2.440 ... (remaining 22395 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 1.750 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.220 Find NCS groups from input model: 0.080 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 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 0.061 2965 Z= 0.316 Angle : 0.921 18.632 4064 Z= 0.508 Chirality : 0.050 0.163 453 Planarity : 0.006 0.062 531 Dihedral : 13.676 77.553 951 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 19.95 % Favored : 79.80 % Rotamer: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.53 % 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: -5.76 (0.31), residues: 396 helix: -4.70 (0.25), residues: 39 sheet: -3.12 (0.39), residues: 117 loop : -4.25 (0.30), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 110 HIS 0.005 0.003 HIS A 519 PHE 0.024 0.002 PHE D 82 TYR 0.017 0.002 TYR E 32 ARG 0.003 0.001 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.334 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1179 time to fit residues: 6.6655 Evaluate side-chains 24 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2965 Z= 0.190 Angle : 0.720 16.164 4064 Z= 0.363 Chirality : 0.048 0.176 453 Planarity : 0.006 0.060 531 Dihedral : 6.871 41.221 430 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 2.96 % Allowed : 15.93 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.87 (0.34), residues: 396 helix: -3.91 (0.57), residues: 33 sheet: -2.59 (0.41), residues: 118 loop : -3.65 (0.32), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 110 HIS 0.007 0.003 HIS E 35 PHE 0.019 0.001 PHE D 82 TYR 0.012 0.002 TYR E 32 ARG 0.002 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 43 average time/residue: 0.1044 time to fit residues: 6.0505 Evaluate side-chains 35 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0314 time to fit residues: 0.7162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 0.0270 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2965 Z= 0.165 Angle : 0.666 14.242 4064 Z= 0.339 Chirality : 0.046 0.155 453 Planarity : 0.005 0.056 531 Dihedral : 6.352 38.230 430 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 2.22 % Allowed : 16.30 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.37), residues: 396 helix: -3.47 (0.64), residues: 33 sheet: -2.23 (0.42), residues: 121 loop : -3.27 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 110 HIS 0.005 0.002 HIS E 35 PHE 0.017 0.001 PHE D 82 TYR 0.009 0.001 TYR E 50 ARG 0.002 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.352 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 44 average time/residue: 0.1231 time to fit residues: 7.0443 Evaluate side-chains 33 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.339 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0323 time to fit residues: 0.5464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 35 optimal weight: 0.0370 chunk 37 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2965 Z= 0.211 Angle : 0.689 14.597 4064 Z= 0.352 Chirality : 0.046 0.143 453 Planarity : 0.006 0.055 531 Dihedral : 6.295 37.224 430 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.90 % Favored : 85.10 % Rotamer: Outliers : 2.59 % Allowed : 19.26 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.37), residues: 396 helix: -3.38 (0.54), residues: 39 sheet: -2.07 (0.44), residues: 120 loop : -3.22 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 110 HIS 0.004 0.002 HIS E 35 PHE 0.028 0.002 PHE E 54 TYR 0.010 0.001 TYR E 50 ARG 0.004 0.001 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.330 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 35 average time/residue: 0.1393 time to fit residues: 6.7086 Evaluate side-chains 31 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.525 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0451 time to fit residues: 0.7924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 0.0770 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 40.0000 chunk 22 optimal weight: 0.0770 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 2965 Z= 0.151 Angle : 0.626 12.845 4064 Z= 0.319 Chirality : 0.046 0.154 453 Planarity : 0.005 0.051 531 Dihedral : 5.718 34.521 430 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 1.48 % Allowed : 21.11 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.39), residues: 396 helix: -3.40 (0.61), residues: 33 sheet: -1.71 (0.45), residues: 120 loop : -2.91 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 110 HIS 0.005 0.002 HIS E 35 PHE 0.016 0.002 PHE E 54 TYR 0.008 0.001 TYR E 50 ARG 0.001 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.331 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 0.1201 time to fit residues: 6.4731 Evaluate side-chains 35 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.335 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0320 time to fit residues: 0.4789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.0470 chunk 31 optimal weight: 0.4980 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 0.0570 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.0000 overall best weight: 0.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 2965 Z= 0.153 Angle : 0.637 11.573 4064 Z= 0.321 Chirality : 0.044 0.155 453 Planarity : 0.005 0.053 531 Dihedral : 5.587 35.990 430 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 1.85 % Allowed : 21.48 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.40), residues: 396 helix: -3.24 (0.67), residues: 33 sheet: -1.40 (0.46), residues: 126 loop : -2.78 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 110 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE E 54 TYR 0.011 0.001 TYR E 50 ARG 0.001 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 46 average time/residue: 0.1142 time to fit residues: 6.8505 Evaluate side-chains 35 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0313 time to fit residues: 0.5399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 0.0670 chunk 37 optimal weight: 0.1980 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 0.0170 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.0158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2965 Z= 0.192 Angle : 0.646 11.870 4064 Z= 0.328 Chirality : 0.045 0.145 453 Planarity : 0.005 0.056 531 Dihedral : 5.576 34.728 430 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 1.11 % Allowed : 24.07 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.40), residues: 396 helix: -3.37 (0.65), residues: 33 sheet: -1.46 (0.45), residues: 125 loop : -2.74 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 110 HIS 0.003 0.002 HIS E 35 PHE 0.025 0.002 PHE E 54 TYR 0.011 0.001 TYR E 50 ARG 0.003 0.001 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 36 average time/residue: 0.1098 time to fit residues: 5.4074 Evaluate side-chains 32 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.305 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0356 time to fit residues: 0.5070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.0870 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2965 Z= 0.213 Angle : 0.661 13.046 4064 Z= 0.335 Chirality : 0.046 0.141 453 Planarity : 0.005 0.056 531 Dihedral : 5.935 34.851 430 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.65 % Favored : 85.35 % Rotamer: Outliers : 1.48 % Allowed : 23.70 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.40), residues: 396 helix: -3.10 (0.61), residues: 39 sheet: -1.53 (0.45), residues: 127 loop : -2.77 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 110 HIS 0.003 0.002 HIS A 519 PHE 0.019 0.002 PHE E 54 TYR 0.013 0.001 TYR E 95 ARG 0.004 0.001 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.1204 time to fit residues: 7.0080 Evaluate side-chains 36 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0320 time to fit residues: 0.6037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 0.0980 chunk 22 optimal weight: 0.3980 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2965 Z= 0.275 Angle : 0.729 13.529 4064 Z= 0.374 Chirality : 0.048 0.158 453 Planarity : 0.006 0.058 531 Dihedral : 6.271 38.810 430 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.40 % Favored : 84.60 % Rotamer: Outliers : 0.74 % Allowed : 25.56 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.40), residues: 396 helix: -3.50 (0.59), residues: 34 sheet: -1.57 (0.45), residues: 125 loop : -2.77 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 110 HIS 0.006 0.003 HIS E 35 PHE 0.017 0.002 PHE E 54 TYR 0.013 0.002 TYR E 33 ARG 0.005 0.001 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 38 average time/residue: 0.1234 time to fit residues: 6.1376 Evaluate side-chains 34 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0315 time to fit residues: 0.4769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 0.0470 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2965 Z= 0.205 Angle : 0.685 12.881 4064 Z= 0.350 Chirality : 0.046 0.163 453 Planarity : 0.005 0.056 531 Dihedral : 5.813 37.374 430 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 1.48 % Allowed : 24.07 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.41), residues: 396 helix: -4.05 (0.43), residues: 34 sheet: -1.32 (0.46), residues: 128 loop : -2.54 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 110 HIS 0.005 0.002 HIS E 35 PHE 0.017 0.001 PHE E 54 TYR 0.010 0.001 TYR E 95 ARG 0.002 0.000 ARG E 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 0.1164 time to fit residues: 6.5902 Evaluate side-chains 38 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0406 time to fit residues: 0.6157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 0.0970 chunk 27 optimal weight: 0.2980 chunk 1 optimal weight: 9.9990 chunk 22 optimal weight: 0.4980 chunk 35 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.094556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.089502 restraints weight = 12080.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.089759 restraints weight = 11012.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.089843 restraints weight = 10173.212| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2965 Z= 0.197 Angle : 0.679 11.804 4064 Z= 0.351 Chirality : 0.046 0.154 453 Planarity : 0.006 0.061 531 Dihedral : 5.562 37.660 430 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 0.37 % Allowed : 24.07 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.41), residues: 396 helix: -3.99 (0.45), residues: 34 sheet: -1.00 (0.47), residues: 126 loop : -2.47 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 110 HIS 0.005 0.003 HIS E 35 PHE 0.016 0.001 PHE E 54 TYR 0.029 0.002 TYR E 33 ARG 0.004 0.001 ARG E 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1040.71 seconds wall clock time: 19 minutes 26.75 seconds (1166.75 seconds total)