Starting phenix.real_space_refine (version: dev) on Tue Feb 21 19:03:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/02_2023/7uin_26550_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/02_2023/7uin_26550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/02_2023/7uin_26550.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/02_2023/7uin_26550.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/02_2023/7uin_26550_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/02_2023/7uin_26550_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.034 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 Process input model Symmetric amino acids flipped Residue "D GLU 30": "OE1" <-> "OE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D ASP 132": "OD1" <-> "OD2" Residue "D PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 147": "OD1" <-> "OD2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 280": "OD1" <-> "OD2" Residue "D ASP 376": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15585 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 11639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 11639 Classifications: {'RNA': 541} Modifications used: {'rna2p_pur': 38, 'rna2p_pyr': 10, 'rna3p_pur': 290, 'rna3p_pyr': 203} Link IDs: {'rna2p': 47, 'rna3p': 493} Chain breaks: 5 Chain: "D" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3133 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 10, 'TRANS': 376} Chain breaks: 2 Chain: "A" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 759 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Unusual residues: {' MG': 28, 'NH4': 2} Classifications: {'undetermined': 30, 'water': 23} Link IDs: {None: 52} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.27, per 1000 atoms: 0.59 Number of scatterers: 15585 At special positions: 0 Unit cell: (99.008, 158.08, 158.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 578 15.00 Mg 28 11.99 O 4543 8.00 N 2869 7.00 C 7546 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: 9.63 Conformation dependent library (CDL) restraints added in 611.4 milliseconds 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 2 sheets defined 61.8% alpha, 5.9% beta 205 base pairs and 342 stacking pairs defined. Time for finding SS restraints: 8.66 Creating SS restraints... Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 39 through 56 removed outlier: 6.802A pdb=" N GLU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 102 Proline residue: D 100 - end of helix Processing helix chain 'D' and resid 119 through 132 Processing helix chain 'D' and resid 145 through 148 No H-bonds generated for 'chain 'D' and resid 145 through 148' Processing helix chain 'D' and resid 151 through 161 Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 197 through 217 removed outlier: 3.917A pdb=" N LEU D 201 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU D 210 " --> pdb=" O MET D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 251 Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 292 through 305 Processing helix chain 'D' and resid 314 through 332 Processing helix chain 'D' and resid 338 through 360 Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 377 through 386 Processing helix chain 'D' and resid 390 through 395 Processing helix chain 'D' and resid 398 through 402 Processing helix chain 'D' and resid 405 through 411 Processing helix chain 'D' and resid 416 through 423 Processing sheet with id= A, first strand: chain 'D' and resid 263 through 265 removed outlier: 3.948A pdb=" N ASN D 220 " --> pdb=" O MET D 231 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 275 through 279 169 hydrogen bonds defined for protein. 501 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 501 hydrogen bonds 792 hydrogen bond angles 0 basepair planarities 205 basepair parallelities 342 stacking parallelities Total time for adding SS restraints: 8.69 Time building geometry restraints manager: 10.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.13: 1 1.13 - 1.43: 9395 1.43 - 1.73: 7647 1.73 - 2.04: 34 2.04 - 2.34: 1 Bond restraints: 17078 Sorted by residual: bond pdb=" CG PRO D 281 " pdb=" CD PRO D 281 " ideal model delta sigma weight residual 1.503 0.828 0.675 3.40e-02 8.65e+02 3.95e+02 bond pdb=" CB PRO D 281 " pdb=" CG PRO D 281 " ideal model delta sigma weight residual 1.492 2.337 -0.845 5.00e-02 4.00e+02 2.86e+02 bond pdb=" N PRO D 281 " pdb=" CD PRO D 281 " ideal model delta sigma weight residual 1.473 1.595 -0.122 1.40e-02 5.10e+03 7.65e+01 bond pdb=" N PRO D 281 " pdb=" CA PRO D 281 " ideal model delta sigma weight residual 1.471 1.397 0.074 1.32e-02 5.74e+03 3.15e+01 bond pdb=" CA PRO D 281 " pdb=" CB PRO D 281 " ideal model delta sigma weight residual 1.534 1.462 0.072 1.40e-02 5.10e+03 2.63e+01 ... (remaining 17073 not shown) Histogram of bond angle deviations from ideal: 0.08 - 29.81: 1 29.81 - 59.54: 0 59.54 - 89.28: 0 89.28 - 119.01: 17403 119.01 - 148.74: 8514 Bond angle restraints: 25918 Sorted by residual: angle pdb=" CB PRO D 281 " pdb=" CG PRO D 281 " pdb=" CD PRO D 281 " ideal model delta sigma weight residual 106.10 0.08 106.02 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO D 281 " pdb=" N PRO D 281 " pdb=" CD PRO D 281 " ideal model delta sigma weight residual 112.00 89.42 22.58 1.40e+00 5.10e-01 2.60e+02 angle pdb=" N PRO D 281 " pdb=" CA PRO D 281 " pdb=" CB PRO D 281 " ideal model delta sigma weight residual 103.48 89.59 13.89 1.00e+00 1.00e+00 1.93e+02 angle pdb=" CA PRO D 62 " pdb=" N PRO D 62 " pdb=" CD PRO D 62 " ideal model delta sigma weight residual 112.00 94.92 17.08 1.40e+00 5.10e-01 1.49e+02 angle pdb=" CA PRO D 281 " pdb=" CB PRO D 281 " pdb=" CG PRO D 281 " ideal model delta sigma weight residual 104.50 90.46 14.04 1.90e+00 2.77e-01 5.46e+01 ... (remaining 25913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 8109 35.84 - 71.68: 611 71.68 - 107.51: 60 107.51 - 143.35: 8 143.35 - 179.19: 10 Dihedral angle restraints: 8798 sinusoidal: 7674 harmonic: 1124 Sorted by residual: dihedral pdb=" O4' U B 2 " pdb=" C1' U B 2 " pdb=" N1 U B 2 " pdb=" C2 U B 2 " ideal model delta sinusoidal sigma weight residual 200.00 46.39 153.61 1 1.50e+01 4.44e-03 8.09e+01 dihedral pdb=" O4' C B 439 " pdb=" C1' C B 439 " pdb=" N1 C B 439 " pdb=" C2 C B 439 " ideal model delta sinusoidal sigma weight residual 200.00 48.62 151.38 1 1.50e+01 4.44e-03 8.01e+01 dihedral pdb=" O4' C B 440 " pdb=" C1' C B 440 " pdb=" N1 C B 440 " pdb=" C2 C B 440 " ideal model delta sinusoidal sigma weight residual 232.00 79.74 152.26 1 1.70e+01 3.46e-03 6.26e+01 ... (remaining 8795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3113 0.087 - 0.175: 179 0.175 - 0.262: 14 0.262 - 0.350: 9 0.350 - 0.437: 3 Chirality restraints: 3318 Sorted by residual: chirality pdb=" CA PRO D 281 " pdb=" N PRO D 281 " pdb=" C PRO D 281 " pdb=" CB PRO D 281 " both_signs ideal model delta sigma weight residual False 2.72 2.28 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CB ILE D 168 " pdb=" CA ILE D 168 " pdb=" CG1 ILE D 168 " pdb=" CG2 ILE D 168 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C1' A B 370 " pdb=" O4' A B 370 " pdb=" C2' A B 370 " pdb=" N9 A B 370 " both_signs ideal model delta sigma weight residual False 2.46 2.08 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 3315 not shown) Planarity restraints: 1121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 47 " 0.032 2.00e-02 2.50e+03 6.26e-02 3.92e+01 pdb=" CG ASN D 47 " -0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN D 47 " 0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN D 47 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 258 " 0.024 2.00e-02 2.50e+03 4.82e-02 2.32e+01 pdb=" CG ASN D 258 " -0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN D 258 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN D 258 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 61 " -0.078 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO D 62 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO D 62 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 62 " -0.058 5.00e-02 4.00e+02 ... (remaining 1118 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 11 2.16 - 2.85: 4627 2.85 - 3.53: 21507 3.53 - 4.22: 52724 4.22 - 4.90: 65838 Nonbonded interactions: 144707 Sorted by model distance: nonbonded pdb=" O3' U B 638 " pdb="MG MG B 701 " model vdw 1.477 2.170 nonbonded pdb=" OP1 C B 581 " pdb="MG MG B 701 " model vdw 1.870 2.170 nonbonded pdb=" OP2 A B 559 " pdb="MG MG B 703 " model vdw 2.041 2.170 nonbonded pdb=" OP1 G B 247 " pdb="MG MG B 705 " model vdw 2.056 2.170 nonbonded pdb=" OP2 A B 157 " pdb="MG MG B 708 " model vdw 2.080 2.170 ... (remaining 144702 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 578 5.49 5 Mg 28 5.21 5 S 21 5.16 5 C 7546 2.51 5 N 2869 2.21 5 O 4543 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.280 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: 0.020 Extract box with map and model: 12.790 Check model and map are aligned: 0.200 Process input model: 54.200 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 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 : 0.010 0.845 17078 Z= 0.690 Angle : 1.206 106.017 25918 Z= 0.554 Chirality : 0.047 0.437 3318 Planarity : 0.009 0.108 1121 Dihedral : 19.722 179.187 8074 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.67 % Favored : 95.80 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: -1.14 (0.37), residues: 381 helix: -0.53 (0.28), residues: 253 sheet: 0.31 (0.92), residues: 24 loop : -1.20 (0.56), residues: 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.778 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 1.3324 time to fit residues: 86.9342 Evaluate side-chains 40 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 1 average time/residue: 1.1172 time to fit residues: 1.9731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.098 17078 Z= 0.238 Angle : 0.659 7.591 25918 Z= 0.341 Chirality : 0.035 0.251 3318 Planarity : 0.007 0.142 1121 Dihedral : 19.055 176.589 7269 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.67 % Favored : 95.80 % Rotamer Outliers : 7.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: 0.02 (0.40), residues: 381 helix: 0.44 (0.30), residues: 257 sheet: 0.43 (0.92), residues: 24 loop : -0.95 (0.60), residues: 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 40 time to evaluate : 0.768 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 7 residues processed: 62 average time/residue: 1.3248 time to fit residues: 90.8916 Evaluate side-chains 45 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.1476 time to fit residues: 1.0640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 29 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 17078 Z= 0.247 Angle : 0.653 8.294 25918 Z= 0.338 Chirality : 0.036 0.267 3318 Planarity : 0.006 0.141 1121 Dihedral : 19.004 177.605 7269 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.15 % Favored : 96.33 % Rotamer Outliers : 7.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.41), residues: 381 helix: 0.77 (0.30), residues: 260 sheet: 0.73 (0.94), residues: 24 loop : -0.92 (0.64), residues: 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 37 time to evaluate : 0.798 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 60 average time/residue: 1.2647 time to fit residues: 84.2551 Evaluate side-chains 48 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.1888 time to fit residues: 1.3586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 86 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 17078 Z= 0.184 Angle : 0.605 7.376 25918 Z= 0.315 Chirality : 0.033 0.235 3318 Planarity : 0.006 0.136 1121 Dihedral : 18.965 178.436 7269 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.41 % Favored : 96.06 % Rotamer Outliers : 7.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: 0.80 (0.41), residues: 381 helix: 1.06 (0.30), residues: 260 sheet: 0.90 (0.96), residues: 24 loop : -0.87 (0.63), residues: 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 42 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 64 average time/residue: 1.2623 time to fit residues: 90.0092 Evaluate side-chains 52 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.784 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.1901 time to fit residues: 1.0727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 128 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 17078 Z= 0.373 Angle : 0.755 9.054 25918 Z= 0.388 Chirality : 0.042 0.265 3318 Planarity : 0.007 0.129 1121 Dihedral : 19.180 175.503 7269 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.67 % Favored : 95.80 % Rotamer Outliers : 5.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 0.19 (0.41), residues: 381 helix: 0.50 (0.29), residues: 258 sheet: 1.39 (1.00), residues: 24 loop : -0.96 (0.65), residues: 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 39 time to evaluate : 0.684 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 55 average time/residue: 1.2133 time to fit residues: 74.6065 Evaluate side-chains 52 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.754 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.6669 time to fit residues: 2.2456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 17078 Z= 0.249 Angle : 0.636 9.027 25918 Z= 0.331 Chirality : 0.036 0.245 3318 Planarity : 0.006 0.126 1121 Dihedral : 18.900 177.571 7269 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.15 % Favored : 96.33 % Rotamer Outliers : 4.99 % 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: 0.50 (0.41), residues: 381 helix: 0.85 (0.30), residues: 260 sheet: 0.93 (0.98), residues: 24 loop : -1.08 (0.65), residues: 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.873 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 14 residues processed: 58 average time/residue: 1.1893 time to fit residues: 77.2323 Evaluate side-chains 52 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 38 time to evaluate : 0.760 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.6879 time to fit residues: 2.3447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 30.0000 chunk 67 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 17078 Z= 0.214 Angle : 0.618 10.263 25918 Z= 0.323 Chirality : 0.034 0.240 3318 Planarity : 0.007 0.148 1121 Dihedral : 18.888 177.594 7269 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.15 % Favored : 96.33 % Rotamer Outliers : 6.74 % 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: 0.61 (0.42), residues: 381 helix: 0.96 (0.30), residues: 257 sheet: 0.80 (1.00), residues: 24 loop : -1.00 (0.65), residues: 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 41 time to evaluate : 0.630 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 59 average time/residue: 1.2707 time to fit residues: 83.9091 Evaluate side-chains 54 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.2029 time to fit residues: 1.3718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 83 optimal weight: 0.0970 chunk 87 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 17078 Z= 0.155 Angle : 0.600 10.484 25918 Z= 0.314 Chirality : 0.032 0.233 3318 Planarity : 0.006 0.122 1121 Dihedral : 18.866 178.000 7269 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.41 % Favored : 96.06 % Rotamer Outliers : 4.99 % 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: 0.74 (0.42), residues: 381 helix: 1.12 (0.31), residues: 257 sheet: 0.29 (0.96), residues: 24 loop : -0.97 (0.65), residues: 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 40 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 55 average time/residue: 1.1714 time to fit residues: 72.4272 Evaluate side-chains 51 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.1847 time to fit residues: 1.0170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 51 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 17078 Z= 0.167 Angle : 0.593 10.980 25918 Z= 0.310 Chirality : 0.032 0.226 3318 Planarity : 0.006 0.121 1121 Dihedral : 18.781 178.426 7269 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.15 % Favored : 96.33 % Rotamer Outliers : 4.99 % 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: 0.99 (0.43), residues: 381 helix: 1.31 (0.31), residues: 260 sheet: 0.17 (0.99), residues: 24 loop : -0.90 (0.67), residues: 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 40 time to evaluate : 0.820 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 54 average time/residue: 1.1796 time to fit residues: 71.5102 Evaluate side-chains 50 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.1893 time to fit residues: 1.0519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 80 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 17078 Z= 0.374 Angle : 0.740 10.971 25918 Z= 0.381 Chirality : 0.042 0.263 3318 Planarity : 0.006 0.119 1121 Dihedral : 18.944 176.413 7269 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.20 % Favored : 95.28 % Rotamer Outliers : 4.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.41), residues: 381 helix: 0.64 (0.30), residues: 257 sheet: 0.71 (1.06), residues: 24 loop : -1.15 (0.63), residues: 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 42 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 56 average time/residue: 1.1743 time to fit residues: 73.9001 Evaluate side-chains 53 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.711 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.1782 time to fit residues: 0.9835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 4 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 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 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.197387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.153812 restraints weight = 20013.125| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 0.91 r_work: 0.3514 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 17078 Z= 0.275 Angle : 0.665 10.817 25918 Z= 0.346 Chirality : 0.037 0.260 3318 Planarity : 0.006 0.118 1121 Dihedral : 18.861 176.631 7269 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.41 % Favored : 96.06 % Rotamer Outliers : 3.81 % 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: 0.37 (0.42), residues: 381 helix: 0.79 (0.31), residues: 257 sheet: 0.78 (1.04), residues: 24 loop : -1.14 (0.64), residues: 100 =============================================================================== Job complete usr+sys time: 3048.66 seconds wall clock time: 56 minutes 14.69 seconds (3374.69 seconds total)