Starting phenix.real_space_refine (version: dev) on Wed Apr 6 14:06:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/04_2022/6mec_9106.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/04_2022/6mec_9106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/04_2022/6mec_9106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/04_2022/6mec_9106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/04_2022/6mec_9106.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/04_2022/6mec_9106.pdb" } resolution = 3.6 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= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C ARG 413": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 21276 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 17537 Classifications: {'RNA': 817, 'DNA': 1} Modifications used: {'rna3p_pyr': 323, 'rna2p_pur': 53, 'rna3p_pur': 407, 'rna2p_pyr': 34} Link IDs: {'rna3p': 730, 'rna2p': 87} Chain breaks: 2 Chain: "B" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 294 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "C" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3393 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 14, 'CIS': 1, 'TRANS': 398} Chain breaks: 2 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Unusual residues: {' NA': 1, ' MG': 50} Classifications: {'undetermined': 51} Link IDs: {None: 50} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.68, per 1000 atoms: 0.60 Number of scatterers: 21276 At special positions: 0 Unit cell: (116.13, 154.05, 237, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 8 16.00 P 832 15.00 Mg 51 11.99 Na 1 11.00 O 6337 8.00 N 3918 7.00 C 10129 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: 12.35 Conformation dependent library (CDL) restraints added in 696.3 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 776 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 3 sheets defined 53.4% alpha, 6.3% beta 279 base pairs and 440 stacking pairs defined. Time for finding SS restraints: 10.23 Creating SS restraints... Processing helix chain 'C' and resid 27 through 48 removed outlier: 4.384A pdb=" N ASN C 32 " --> pdb=" O TRP C 28 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ARG C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU C 48 " --> pdb=" O LYS C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 93 through 105 removed outlier: 4.176A pdb=" N LEU C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 154 Proline residue: C 149 - end of helix removed outlier: 3.567A pdb=" N THR C 153 " --> pdb=" O PRO C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 179 removed outlier: 3.535A pdb=" N ALA C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 212 through 222 Processing helix chain 'C' and resid 243 through 252 removed outlier: 3.752A pdb=" N LEU C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 285 through 300 removed outlier: 3.520A pdb=" N GLU C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 356 Processing helix chain 'C' and resid 360 through 378 Proline residue: C 370 - end of helix Processing helix chain 'C' and resid 384 through 406 Processing helix chain 'C' and resid 411 through 420 Processing helix chain 'C' and resid 448 through 452 removed outlier: 3.837A pdb=" N THR C 452 " --> pdb=" O ALA C 449 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 115 through 119 removed outlier: 3.994A pdb=" N VAL C 117 " --> pdb=" O LEU C 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 270 through 273 removed outlier: 4.190A pdb=" N PHE C 277 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 191 " --> pdb=" O PHE C 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 319 through 321 163 hydrogen bonds defined for protein. 465 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 725 hydrogen bonds 1260 hydrogen bond angles 0 basepair planarities 279 basepair parallelities 440 stacking parallelities Total time for adding SS restraints: 15.67 Time building geometry restraints manager: 13.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2006 1.32 - 1.44: 11160 1.44 - 1.56: 8588 1.56 - 1.68: 1663 1.68 - 1.80: 12 Bond restraints: 23429 Sorted by residual: bond pdb=" N PRO C 132 " pdb=" CD PRO C 132 " ideal model delta sigma weight residual 1.473 1.416 0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" N PRO C 245 " pdb=" CD PRO C 245 " ideal model delta sigma weight residual 1.473 1.430 0.043 1.40e-02 5.10e+03 9.60e+00 bond pdb=" CB ASN C 389 " pdb=" CG ASN C 389 " ideal model delta sigma weight residual 1.516 1.446 0.070 2.50e-02 1.60e+03 7.74e+00 bond pdb=" CB ARG C 406 " pdb=" CG ARG C 406 " ideal model delta sigma weight residual 1.520 1.438 0.082 3.00e-02 1.11e+03 7.49e+00 bond pdb=" CE3 TRP C 402 " pdb=" CZ3 TRP C 402 " ideal model delta sigma weight residual 1.382 1.303 0.079 3.00e-02 1.11e+03 6.89e+00 ... (remaining 23424 not shown) Histogram of bond angle deviations from ideal: 94.17 - 102.87: 1653 102.87 - 111.56: 14206 111.56 - 120.26: 11824 120.26 - 128.95: 7268 128.95 - 137.65: 841 Bond angle restraints: 35792 Sorted by residual: angle pdb=" C3' A A 481 " pdb=" O3' A A 481 " pdb=" P U A 482 " ideal model delta sigma weight residual 120.20 128.24 -8.04 1.50e+00 4.44e-01 2.87e+01 angle pdb=" C3' U A 545 " pdb=" O3' U A 545 " pdb=" P C A 546 " ideal model delta sigma weight residual 120.20 127.78 -7.58 1.50e+00 4.44e-01 2.55e+01 angle pdb=" C3' A A 462 " pdb=" O3' A A 462 " pdb=" P U A 463 " ideal model delta sigma weight residual 120.20 127.58 -7.38 1.50e+00 4.44e-01 2.42e+01 angle pdb=" O3' A A 12 " pdb=" C3' A A 12 " pdb=" C2' A A 12 " ideal model delta sigma weight residual 113.70 120.85 -7.15 1.50e+00 4.44e-01 2.27e+01 angle pdb=" C3' C A 666 " pdb=" O3' C A 666 " pdb=" P A A 667 " ideal model delta sigma weight residual 120.20 127.31 -7.11 1.50e+00 4.44e-01 2.24e+01 ... (remaining 35787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 11212 35.58 - 71.16: 732 71.16 - 106.74: 76 106.74 - 142.33: 8 142.33 - 177.91: 10 Dihedral angle restraints: 12038 sinusoidal: 10840 harmonic: 1198 Sorted by residual: dihedral pdb=" O4' U A 258 " pdb=" C1' U A 258 " pdb=" N1 U A 258 " pdb=" C2 U A 258 " ideal model delta sinusoidal sigma weight residual -128.00 49.91 -177.91 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A 839 " pdb=" C1' U A 839 " pdb=" N1 U A 839 " pdb=" C2 U A 839 " ideal model delta sinusoidal sigma weight residual -128.00 45.05 -173.05 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" CA TYR C 273 " pdb=" C TYR C 273 " pdb=" N ALA C 274 " pdb=" CA ALA C 274 " ideal model delta harmonic sigma weight residual -180.00 -140.17 -39.83 0 5.00e+00 4.00e-02 6.35e+01 ... (remaining 12035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4117 0.088 - 0.175: 475 0.175 - 0.263: 40 0.263 - 0.351: 8 0.351 - 0.439: 4 Chirality restraints: 4644 Sorted by residual: chirality pdb=" C1' A A 401 " pdb=" O4' A A 401 " pdb=" C2' A A 401 " pdb=" N9 A A 401 " both_signs ideal model delta sigma weight residual False 2.44 2.00 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" C3' G A 8 " pdb=" C4' G A 8 " pdb=" O3' G A 8 " pdb=" C2' G A 8 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C3' G A 832 " pdb=" C4' G A 832 " pdb=" O3' G A 832 " pdb=" C2' G A 832 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.40e+00 ... (remaining 4641 not shown) Planarity restraints: 1417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 238 " -0.049 2.00e-02 2.50e+03 2.15e-02 1.27e+01 pdb=" N9 A A 238 " 0.047 2.00e-02 2.50e+03 pdb=" C8 A A 238 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A A 238 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A 238 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A A 238 " -0.008 2.00e-02 2.50e+03 pdb=" N6 A A 238 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A A 238 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A A 238 " 0.005 2.00e-02 2.50e+03 pdb=" N3 A A 238 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A A 238 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 407 " 0.057 5.00e-02 4.00e+02 8.68e-02 1.20e+01 pdb=" N PRO C 408 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 408 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 408 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A 401 " 0.044 2.00e-02 2.50e+03 1.84e-02 9.34e+00 pdb=" N9 A A 401 " -0.035 2.00e-02 2.50e+03 pdb=" C8 A A 401 " -0.007 2.00e-02 2.50e+03 pdb=" N7 A A 401 " -0.005 2.00e-02 2.50e+03 pdb=" C5 A A 401 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A A 401 " 0.010 2.00e-02 2.50e+03 pdb=" N6 A A 401 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A A 401 " 0.008 2.00e-02 2.50e+03 pdb=" C2 A A 401 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A A 401 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A A 401 " -0.015 2.00e-02 2.50e+03 ... (remaining 1414 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 75 2.31 - 2.96: 9335 2.96 - 3.60: 36914 3.60 - 4.25: 64238 4.25 - 4.90: 82886 Nonbonded interactions: 193448 Sorted by model distance: nonbonded pdb=" CZ2 TRP C 28 " pdb=" CD LYS C 73 " model vdw 1.659 3.740 nonbonded pdb=" NE ARG C 380 " pdb=" OE1 GLN C 455 " model vdw 1.667 2.520 nonbonded pdb=" P U A 1 " pdb=" O2' A A 860 " model vdw 1.676 3.400 nonbonded pdb=" O LEU C 356 " pdb=" CH2 TRP C 402 " model vdw 1.793 3.340 nonbonded pdb=" O2' A A 428 " pdb=" OP1 A A 429 " model vdw 1.851 2.440 ... (remaining 193443 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: 7 Type Number sf(0) Gaussians P 832 5.49 5 Mg 51 5.21 5 S 8 5.16 5 Na 1 4.78 5 C 10129 2.51 5 N 3918 2.21 5 O 6337 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 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: 14.450 Check model and map are aligned: 0.360 Convert atoms to be neutral: 0.210 Process input model: 75.670 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 0.099 23429 Z= 0.612 Angle : 1.213 12.467 35792 Z= 0.589 Chirality : 0.058 0.439 4644 Planarity : 0.008 0.087 1417 Dihedral : 18.236 177.907 11262 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.73 % Favored : 86.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.93 (0.32), residues: 408 helix: -3.26 (0.23), residues: 212 sheet: -1.60 (0.94), residues: 34 loop : -3.49 (0.42), residues: 162 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.005 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.4551 time to fit residues: 66.4775 Evaluate side-chains 48 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 HIS C 269 ASN C 341 ASN C 346 HIS ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 HIS ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 23429 Z= 0.217 Angle : 0.692 9.004 35792 Z= 0.348 Chirality : 0.036 0.281 4644 Planarity : 0.005 0.051 1417 Dihedral : 18.345 179.576 10399 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer Outliers : 2.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.37), residues: 408 helix: -1.58 (0.31), residues: 216 sheet: -1.46 (0.85), residues: 34 loop : -3.22 (0.44), residues: 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 1.076 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 0.4113 time to fit residues: 45.3777 Evaluate side-chains 61 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1882 time to fit residues: 3.2998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 110 optimal weight: 0.0040 chunk 38 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN C 94 GLN C 341 ASN ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 23429 Z= 0.191 Angle : 0.628 9.190 35792 Z= 0.315 Chirality : 0.032 0.268 4644 Planarity : 0.005 0.045 1417 Dihedral : 17.968 179.474 10399 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.41), residues: 408 helix: -0.34 (0.34), residues: 215 sheet: -1.00 (0.83), residues: 34 loop : -3.09 (0.48), residues: 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 1.001 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 0.4444 time to fit residues: 42.0118 Evaluate side-chains 53 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3052 time to fit residues: 2.7920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN C 379 HIS ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 23429 Z= 0.171 Angle : 0.592 8.756 35792 Z= 0.296 Chirality : 0.031 0.261 4644 Planarity : 0.004 0.031 1417 Dihedral : 17.761 179.517 10399 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.42), residues: 408 helix: 0.12 (0.35), residues: 214 sheet: -1.02 (0.82), residues: 34 loop : -2.89 (0.50), residues: 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 1.000 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 0.3840 time to fit residues: 36.5088 Evaluate side-chains 55 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2708 time to fit residues: 2.6111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 GLN ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.168 23429 Z= 0.246 Angle : 0.641 12.113 35792 Z= 0.322 Chirality : 0.032 0.262 4644 Planarity : 0.005 0.040 1417 Dihedral : 17.821 179.429 10399 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.42), residues: 408 helix: 0.17 (0.35), residues: 214 sheet: -0.50 (0.87), residues: 32 loop : -3.01 (0.51), residues: 162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 1.000 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 59 average time/residue: 0.4037 time to fit residues: 36.0825 Evaluate side-chains 57 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2074 time to fit residues: 3.6324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 269 ASN C 346 HIS ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 23429 Z= 0.293 Angle : 0.687 10.500 35792 Z= 0.343 Chirality : 0.035 0.274 4644 Planarity : 0.005 0.045 1417 Dihedral : 17.992 179.463 10399 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.42), residues: 408 helix: 0.10 (0.35), residues: 214 sheet: -0.47 (0.87), residues: 32 loop : -3.14 (0.50), residues: 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.939 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 55 average time/residue: 0.3738 time to fit residues: 31.6961 Evaluate side-chains 49 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2120 time to fit residues: 2.0262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 118 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 23429 Z= 0.300 Angle : 0.689 9.647 35792 Z= 0.344 Chirality : 0.035 0.275 4644 Planarity : 0.005 0.048 1417 Dihedral : 18.004 179.499 10399 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.41), residues: 408 helix: 0.06 (0.35), residues: 214 sheet: -0.36 (0.89), residues: 32 loop : -3.26 (0.48), residues: 162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.994 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 0.3581 time to fit residues: 29.5201 Evaluate side-chains 53 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2093 time to fit residues: 2.3730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 23429 Z= 0.287 Angle : 0.680 10.283 35792 Z= 0.340 Chirality : 0.035 0.274 4644 Planarity : 0.005 0.048 1417 Dihedral : 18.009 179.552 10399 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.42), residues: 408 helix: 0.11 (0.35), residues: 213 sheet: -0.18 (0.97), residues: 32 loop : -3.25 (0.47), residues: 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 1.076 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 49 average time/residue: 0.3916 time to fit residues: 29.3461 Evaluate side-chains 47 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1912 time to fit residues: 1.5949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 104 optimal weight: 0.0170 chunk 72 optimal weight: 10.0000 chunk 116 optimal weight: 0.7980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 23429 Z= 0.139 Angle : 0.574 10.653 35792 Z= 0.286 Chirality : 0.029 0.273 4644 Planarity : 0.004 0.031 1417 Dihedral : 17.580 179.539 10399 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.42), residues: 408 helix: 0.57 (0.35), residues: 217 sheet: -0.80 (0.90), residues: 34 loop : -3.18 (0.47), residues: 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.3785 time to fit residues: 31.1813 Evaluate side-chains 47 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 0.0010 chunk 112 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.740 23429 Z= 0.499 Angle : 0.865 106.026 35792 Z= 0.386 Chirality : 0.032 0.435 4644 Planarity : 0.004 0.044 1417 Dihedral : 17.577 179.558 10399 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.42), residues: 408 helix: 0.51 (0.35), residues: 217 sheet: -0.83 (0.89), residues: 34 loop : -3.18 (0.47), residues: 157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.3749 time to fit residues: 29.2209 Evaluate side-chains 51 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1958 time to fit residues: 1.6317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 100 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 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 = 0.4002 r_free = 0.4002 target = 0.126168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.099851 restraints weight = 58673.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.100244 restraints weight = 51499.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.100584 restraints weight = 33791.611| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.740 23429 Z= 0.499 Angle : 0.865 106.026 35792 Z= 0.386 Chirality : 0.032 0.435 4644 Planarity : 0.004 0.044 1417 Dihedral : 17.577 179.558 10399 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.42), residues: 408 helix: 0.51 (0.35), residues: 217 sheet: -0.83 (0.89), residues: 34 loop : -3.18 (0.47), residues: 157 =============================================================================== Job complete usr+sys time: 2248.71 seconds wall clock time: 43 minutes 54.60 seconds (2634.60 seconds total)