Starting phenix.real_space_refine on Thu Dec 7 14:12:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/12_2023/5lii_4053.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/12_2023/5lii_4053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/12_2023/5lii_4053.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/12_2023/5lii_4053.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/12_2023/5lii_4053.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/12_2023/5lii_4053.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.270 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 1947 2.51 5 N 545 2.21 5 O 595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3098 Number of models: 1 Model: "" Number of chains: 1 Chain: "P" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3098 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PCIS': 4, 'PTRANS': 14, 'TRANS': 414} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 154 Time building chain proxies: 1.37, per 1000 atoms: 0.44 Number of scatterers: 3098 At special positions: 0 Unit cell: (66.24, 100.74, 97.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 11 16.00 O 595 8.00 N 545 7.00 C 1947 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: 0.75 Conformation dependent library (CDL) restraints added in 379.9 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 806 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 5 sheets defined 11.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'P' and resid 63 through 68 Processing helix chain 'P' and resid 125 through 131 Processing helix chain 'P' and resid 137 through 159 removed outlier: 3.620A pdb=" N THR P 142 " --> pdb=" O SER P 138 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU P 154 " --> pdb=" O ALA P 150 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR P 159 " --> pdb=" O TRP P 155 " (cutoff:3.500A) Processing helix chain 'P' and resid 197 through 210 removed outlier: 3.528A pdb=" N ASN P 201 " --> pdb=" O GLU P 197 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY P 210 " --> pdb=" O ARG P 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 70 through 72 removed outlier: 6.829A pdb=" N ARG P 71 " --> pdb=" O GLU P 418 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 82 through 84 Processing sheet with id=AA3, first strand: chain 'P' and resid 325 through 326 removed outlier: 3.509A pdb=" N SER P 326 " --> pdb=" O ILE P 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'P' and resid 348 through 350 Processing sheet with id=AA5, first strand: chain 'P' and resid 404 through 407 41 hydrogen bonds defined for protein. 114 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.39 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 542 1.27 - 1.41: 749 1.41 - 1.55: 1832 1.55 - 1.69: 3 1.69 - 1.83: 22 Bond restraints: 3148 Sorted by residual: bond pdb=" C ALA P 101 " pdb=" N PRO P 102 " ideal model delta sigma weight residual 1.334 1.134 0.200 2.34e-02 1.83e+03 7.32e+01 bond pdb=" CA MET P 409 " pdb=" CB MET P 409 " ideal model delta sigma weight residual 1.528 1.420 0.109 1.35e-02 5.49e+03 6.47e+01 bond pdb=" CB TYR P 441 " pdb=" CG TYR P 441 " ideal model delta sigma weight residual 1.512 1.445 0.067 2.20e-02 2.07e+03 9.31e+00 bond pdb=" CG LEU P 181 " pdb=" CD1 LEU P 181 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.04e+00 bond pdb=" CB PRO P 137 " pdb=" CG PRO P 137 " ideal model delta sigma weight residual 1.506 1.400 0.106 3.90e-02 6.57e+02 7.41e+00 ... (remaining 3143 not shown) Histogram of bond angle deviations from ideal: 65.95 - 85.26: 4 85.26 - 104.56: 78 104.56 - 123.86: 4090 123.86 - 143.16: 112 143.16 - 162.47: 2 Bond angle restraints: 4286 Sorted by residual: angle pdb=" N PRO P 399 " pdb=" CA PRO P 399 " pdb=" CB PRO P 399 " ideal model delta sigma weight residual 102.60 65.95 36.65 1.10e+00 8.26e-01 1.11e+03 angle pdb=" N VAL P 118 " pdb=" CA VAL P 118 " pdb=" CB VAL P 118 " ideal model delta sigma weight residual 110.49 78.16 32.33 1.15e+00 7.56e-01 7.90e+02 angle pdb=" N LEU P 398 " pdb=" CA LEU P 398 " pdb=" C LEU P 398 " ideal model delta sigma weight residual 107.91 149.33 -41.42 2.05e+00 2.38e-01 4.08e+02 angle pdb=" N PRO P 399 " pdb=" CD PRO P 399 " pdb=" CG PRO P 399 " ideal model delta sigma weight residual 103.80 79.83 23.97 1.20e+00 6.94e-01 3.99e+02 angle pdb=" N PRO P 399 " pdb=" CA PRO P 399 " pdb=" C PRO P 399 " ideal model delta sigma weight residual 112.10 162.47 -50.37 2.60e+00 1.48e-01 3.75e+02 ... (remaining 4281 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 10.87: 1509 10.87 - 21.73: 277 21.73 - 32.60: 73 32.60 - 43.46: 16 43.46 - 54.32: 6 Dihedral angle restraints: 1881 sinusoidal: 631 harmonic: 1250 Sorted by residual: dihedral pdb=" N VAL P 118 " pdb=" C VAL P 118 " pdb=" CA VAL P 118 " pdb=" CB VAL P 118 " ideal model delta harmonic sigma weight residual 123.40 88.32 35.08 0 2.50e+00 1.60e-01 1.97e+02 dihedral pdb=" CA LYS P 394 " pdb=" C LYS P 394 " pdb=" N ASN P 395 " pdb=" CA ASN P 395 " ideal model delta harmonic sigma weight residual 180.00 -129.42 -50.58 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" N LEU P 398 " pdb=" C LEU P 398 " pdb=" CA LEU P 398 " pdb=" CB LEU P 398 " ideal model delta harmonic sigma weight residual 122.80 144.26 -21.46 0 2.50e+00 1.60e-01 7.37e+01 ... (remaining 1878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.366: 500 0.366 - 0.732: 1 0.732 - 1.098: 1 1.098 - 1.464: 0 1.464 - 1.829: 2 Chirality restraints: 504 Sorted by residual: chirality pdb=" CA PRO P 399 " pdb=" N PRO P 399 " pdb=" C PRO P 399 " pdb=" CB PRO P 399 " both_signs ideal model delta sigma weight residual False 2.72 0.89 1.83 2.00e-01 2.50e+01 8.37e+01 chirality pdb=" CA LEU P 398 " pdb=" N LEU P 398 " pdb=" C LEU P 398 " pdb=" CB LEU P 398 " both_signs ideal model delta sigma weight residual False 2.51 0.99 1.52 2.00e-01 2.50e+01 5.79e+01 chirality pdb=" CA ASN P 133 " pdb=" N ASN P 133 " pdb=" C ASN P 133 " pdb=" CB ASN P 133 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 501 not shown) Planarity restraints: 564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU P 398 " 0.143 5.00e-02 4.00e+02 2.09e-01 7.02e+01 pdb=" N PRO P 399 " -0.359 5.00e-02 4.00e+02 pdb=" CA PRO P 399 " 0.147 5.00e-02 4.00e+02 pdb=" CD PRO P 399 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 261 " 0.029 2.00e-02 2.50e+03 2.01e-02 7.10e+00 pdb=" CG PHE P 261 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE P 261 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE P 261 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE P 261 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE P 261 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE P 261 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 256 " 0.023 2.00e-02 2.50e+03 1.86e-02 6.89e+00 pdb=" CG TYR P 256 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR P 256 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR P 256 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR P 256 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR P 256 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR P 256 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR P 256 " -0.001 2.00e-02 2.50e+03 ... (remaining 561 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 45 2.46 - 3.07: 2532 3.07 - 3.68: 4232 3.68 - 4.29: 5645 4.29 - 4.90: 8788 Nonbonded interactions: 21242 Sorted by model distance: nonbonded pdb=" O ASN P 229 " pdb=" OD1 ASN P 229 " model vdw 1.855 3.040 nonbonded pdb=" CE2 TYR P 117 " pdb=" CG2 THR P 152 " model vdw 1.987 3.760 nonbonded pdb=" O LEU P 398 " pdb=" CD PRO P 399 " model vdw 2.081 2.752 nonbonded pdb=" O GLY P 233 " pdb=" NH1 ARG P 234 " model vdw 2.082 2.520 nonbonded pdb=" OG SER P 75 " pdb=" O VAL P 78 " model vdw 2.093 2.440 ... (remaining 21237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 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: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 8.520 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 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 : 0.015 0.200 3148 Z= 0.963 Angle : 2.407 50.367 4286 Z= 1.473 Chirality : 0.139 1.829 504 Planarity : 0.012 0.209 564 Dihedral : 12.691 54.322 1075 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 42.83 Ramachandran Plot: Outliers : 1.16 % Allowed : 16.94 % Favored : 81.90 % Rotamer: Outliers : 1.41 % Allowed : 6.01 % Favored : 92.58 % Cbeta Deviations : 1.49 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 16.67 % Twisted General : 1.93 % 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: -6.10 (0.25), residues: 431 helix: -4.70 (0.36), residues: 55 sheet: -1.38 (0.90), residues: 28 loop : -4.65 (0.20), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP P 440 HIS 0.011 0.005 HIS P 86 PHE 0.044 0.006 PHE P 94 TYR 0.046 0.005 TYR P 256 ARG 0.010 0.002 ARG P 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 84 average time/residue: 0.0935 time to fit residues: 9.5699 Evaluate side-chains 54 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.217 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0202 time to fit residues: 0.3661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.0170 chunk 25 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 82 GLN P 229 ASN ** P 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3148 Z= 0.233 Angle : 0.910 10.239 4286 Z= 0.484 Chirality : 0.049 0.194 504 Planarity : 0.006 0.052 564 Dihedral : 9.399 33.558 459 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.23 % Favored : 86.08 % Rotamer: Outliers : 6.01 % Allowed : 12.37 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.38 (0.30), residues: 431 helix: -2.57 (0.63), residues: 54 sheet: -0.93 (1.23), residues: 23 loop : -4.39 (0.23), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 452 HIS 0.002 0.001 HIS P 265 PHE 0.018 0.002 PHE P 373 TYR 0.025 0.003 TYR P 441 ARG 0.002 0.001 ARG P 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 0.216 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 78 average time/residue: 0.0999 time to fit residues: 9.4557 Evaluate side-chains 64 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.215 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0440 time to fit residues: 0.7814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 82 GLN ** P 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3148 Z= 0.193 Angle : 0.816 12.479 4286 Z= 0.428 Chirality : 0.047 0.160 504 Planarity : 0.006 0.098 564 Dihedral : 8.062 28.692 459 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.69 % Favored : 85.61 % Rotamer: Outliers : 4.59 % Allowed : 18.37 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -5.25 (0.31), residues: 431 helix: -2.46 (0.63), residues: 61 sheet: -0.82 (1.04), residues: 28 loop : -4.37 (0.24), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP P 57 HIS 0.004 0.001 HIS P 415 PHE 0.012 0.002 PHE P 175 TYR 0.016 0.002 TYR P 441 ARG 0.004 0.000 ARG P 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.214 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 74 average time/residue: 0.1043 time to fit residues: 9.2500 Evaluate side-chains 60 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.215 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0783 time to fit residues: 0.7642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.0870 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 194 GLN P 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3148 Z= 0.170 Angle : 0.771 12.407 4286 Z= 0.395 Chirality : 0.045 0.132 504 Planarity : 0.006 0.089 564 Dihedral : 7.232 28.230 459 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.70 % Allowed : 12.06 % Favored : 87.24 % Rotamer: Outliers : 5.65 % Allowed : 21.91 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.97 (0.31), residues: 431 helix: -2.34 (0.60), residues: 61 sheet: -0.63 (1.04), residues: 28 loop : -4.15 (0.24), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP P 57 HIS 0.001 0.000 HIS P 91 PHE 0.015 0.002 PHE P 373 TYR 0.015 0.002 TYR P 117 ARG 0.002 0.000 ARG P 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.214 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 75 average time/residue: 0.0866 time to fit residues: 8.0605 Evaluate side-chains 63 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.214 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0212 time to fit residues: 0.5924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 35 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3148 Z= 0.230 Angle : 0.800 12.923 4286 Z= 0.415 Chirality : 0.046 0.146 504 Planarity : 0.006 0.089 564 Dihedral : 7.312 25.652 459 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.70 % Allowed : 16.94 % Favored : 82.37 % Rotamer: Outliers : 3.18 % Allowed : 24.38 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.84 (0.32), residues: 431 helix: -2.29 (0.58), residues: 61 sheet: -0.52 (1.06), residues: 28 loop : -4.03 (0.25), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP P 57 HIS 0.002 0.001 HIS P 91 PHE 0.017 0.002 PHE P 261 TYR 0.017 0.002 TYR P 441 ARG 0.002 0.000 ARG P 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.214 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 61 average time/residue: 0.0828 time to fit residues: 6.3909 Evaluate side-chains 58 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.214 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0214 time to fit residues: 0.4805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3148 Z= 0.223 Angle : 0.800 12.923 4286 Z= 0.412 Chirality : 0.046 0.160 504 Planarity : 0.006 0.085 564 Dihedral : 7.255 25.922 459 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.70 % Allowed : 16.71 % Favored : 82.60 % Rotamer: Outliers : 3.89 % Allowed : 25.09 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.67 (0.32), residues: 431 helix: -1.69 (0.66), residues: 54 sheet: -0.59 (1.04), residues: 28 loop : -3.96 (0.25), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP P 57 HIS 0.003 0.001 HIS P 91 PHE 0.021 0.002 PHE P 373 TYR 0.017 0.002 TYR P 441 ARG 0.003 0.000 ARG P 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.214 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 60 average time/residue: 0.0756 time to fit residues: 5.8650 Evaluate side-chains 55 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.214 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0206 time to fit residues: 0.4414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3148 Z= 0.190 Angle : 0.769 13.144 4286 Z= 0.392 Chirality : 0.044 0.150 504 Planarity : 0.007 0.112 564 Dihedral : 6.986 25.887 459 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.70 % Allowed : 15.78 % Favored : 83.53 % Rotamer: Outliers : 2.12 % Allowed : 26.86 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.56 (0.33), residues: 431 helix: -1.89 (0.62), residues: 61 sheet: -0.34 (1.13), residues: 28 loop : -3.88 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP P 57 HIS 0.002 0.001 HIS P 91 PHE 0.013 0.002 PHE P 373 TYR 0.015 0.002 TYR P 218 ARG 0.003 0.000 ARG P 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.214 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 0.0852 time to fit residues: 6.2558 Evaluate side-chains 53 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.215 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1137 time to fit residues: 0.6864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 37 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3148 Z= 0.185 Angle : 0.784 13.615 4286 Z= 0.394 Chirality : 0.044 0.149 504 Planarity : 0.006 0.103 564 Dihedral : 6.823 24.895 459 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.70 % Allowed : 15.55 % Favored : 83.76 % Rotamer: Outliers : 2.12 % Allowed : 29.33 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.51 (0.33), residues: 431 helix: -1.77 (0.63), residues: 61 sheet: -0.55 (1.08), residues: 28 loop : -3.83 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP P 57 HIS 0.001 0.000 HIS P 415 PHE 0.014 0.002 PHE P 373 TYR 0.014 0.002 TYR P 218 ARG 0.001 0.000 ARG P 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.214 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 58 average time/residue: 0.0982 time to fit residues: 7.0277 Evaluate side-chains 56 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.214 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0215 time to fit residues: 0.3707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.0030 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3148 Z= 0.184 Angle : 0.766 13.268 4286 Z= 0.383 Chirality : 0.044 0.145 504 Planarity : 0.007 0.109 564 Dihedral : 6.676 23.971 459 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.70 % Allowed : 15.08 % Favored : 84.22 % Rotamer: Outliers : 0.71 % Allowed : 30.74 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.33 (0.34), residues: 431 helix: -1.55 (0.66), residues: 58 sheet: -0.44 (1.12), residues: 28 loop : -3.70 (0.27), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP P 57 HIS 0.001 0.001 HIS P 224 PHE 0.016 0.002 PHE P 373 TYR 0.014 0.002 TYR P 117 ARG 0.006 0.000 ARG P 377 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.214 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 55 average time/residue: 0.0919 time to fit residues: 6.2956 Evaluate side-chains 52 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.212 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0200 time to fit residues: 0.3298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3148 Z= 0.195 Angle : 0.778 14.163 4286 Z= 0.387 Chirality : 0.044 0.149 504 Planarity : 0.007 0.112 564 Dihedral : 6.621 21.797 459 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.70 % Allowed : 15.31 % Favored : 83.99 % Rotamer: Outliers : 1.06 % Allowed : 30.74 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.30 (0.35), residues: 431 helix: -1.54 (0.66), residues: 58 sheet: -0.36 (1.12), residues: 28 loop : -3.69 (0.27), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP P 57 HIS 0.001 0.001 HIS P 91 PHE 0.016 0.002 PHE P 373 TYR 0.015 0.002 TYR P 460 ARG 0.005 0.000 ARG P 377 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.214 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 0.0862 time to fit residues: 5.6849 Evaluate side-chains 54 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.213 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0209 time to fit residues: 0.3696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.0070 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.199799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.186237 restraints weight = 4953.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.188759 restraints weight = 2907.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.190635 restraints weight = 1933.645| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3148 Z= 0.185 Angle : 0.737 13.102 4286 Z= 0.373 Chirality : 0.043 0.145 504 Planarity : 0.006 0.108 564 Dihedral : 6.472 21.946 459 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.70 % Allowed : 14.62 % Favored : 84.69 % Rotamer: Outliers : 1.06 % Allowed : 30.04 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.22 (0.35), residues: 431 helix: -1.43 (0.65), residues: 58 sheet: -0.30 (1.13), residues: 28 loop : -3.64 (0.27), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP P 57 HIS 0.001 0.000 HIS P 91 PHE 0.016 0.002 PHE P 373 TYR 0.018 0.002 TYR P 460 ARG 0.005 0.000 ARG P 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 705.01 seconds wall clock time: 12 minutes 35.01 seconds (755.01 seconds total)