Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:56:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul4_26591/11_2022/7ul4_26591_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul4_26591/11_2022/7ul4_26591.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul4_26591/11_2022/7ul4_26591_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul4_26591/11_2022/7ul4_26591_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul4_26591/11_2022/7ul4_26591_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul4_26591/11_2022/7ul4_26591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul4_26591/11_2022/7ul4_26591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul4_26591/11_2022/7ul4_26591_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul4_26591/11_2022/7ul4_26591_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.069 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 "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 2524 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2076 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 130 Chain: "D" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 413 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'TRANS': 64} Chain breaks: 4 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {'NG0': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Time building chain proxies: 2.05, per 1000 atoms: 0.81 Number of scatterers: 2524 At special positions: 0 Unit cell: (68.5483, 59.8713, 102.389, 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 22 16.00 O 435 8.00 N 409 7.00 C 1658 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 217 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 410.2 milliseconds 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 670 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 3 sheets defined 67.2% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 66 through 95 removed outlier: 3.590A pdb=" N MET A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 102 through 119 Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 137 through 170 removed outlier: 3.846A pdb=" N MET A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 removed outlier: 4.660A pdb=" N ASP A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 205 removed outlier: 4.034A pdb=" N ALA A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 226 through 239 removed outlier: 3.717A pdb=" N LEU A 232 " --> pdb=" O TRP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 261 removed outlier: 3.867A pdb=" N SER A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 304 Proline residue: A 295 - end of helix removed outlier: 3.592A pdb=" N ILE A 301 " --> pdb=" O HIS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 339 removed outlier: 4.520A pdb=" N SER A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N CYS A 330 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 3.543A pdb=" N ALA A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 351 Processing sheet with id= A, first strand: chain 'A' and resid 207 through 210 Processing sheet with id= B, first strand: chain 'D' and resid 406 through 408 removed outlier: 3.884A pdb=" N VAL D 463 " --> pdb=" O CYS D 407 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 434 through 436 removed outlier: 3.524A pdb=" N ALA D 434 " --> pdb=" O TRP D 421 " (cutoff:3.500A) 186 hydrogen bonds defined for protein. 540 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: 0.73 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 387 1.30 - 1.43: 703 1.43 - 1.56: 1449 1.56 - 1.68: 3 1.68 - 1.81: 32 Bond restraints: 2574 Sorted by residual: bond pdb=" C5 NG0 A 900 " pdb=" C6 NG0 A 900 " ideal model delta sigma weight residual 1.386 1.535 -0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" C3 NG0 A 900 " pdb=" C4 NG0 A 900 " ideal model delta sigma weight residual 1.386 1.533 -0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C1 NG0 A 900 " pdb=" C2 NG0 A 900 " ideal model delta sigma weight residual 1.385 1.528 -0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" C20 NG0 A 900 " pdb=" C21 NG0 A 900 " ideal model delta sigma weight residual 1.385 1.524 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" C18 NG0 A 900 " pdb=" C19 NG0 A 900 " ideal model delta sigma weight residual 1.385 1.523 -0.138 2.00e-02 2.50e+03 4.78e+01 ... (remaining 2569 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.47: 58 106.47 - 113.37: 1408 113.37 - 120.26: 1007 120.26 - 127.16: 1026 127.16 - 134.06: 32 Bond angle restraints: 3531 Sorted by residual: angle pdb=" C3 NG0 A 900 " pdb=" C2 NG0 A 900 " pdb=" O1 NG0 A 900 " ideal model delta sigma weight residual 105.47 120.41 -14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" CA THR A 101 " pdb=" C THR A 101 " pdb=" O THR A 101 " ideal model delta sigma weight residual 121.45 116.48 4.97 1.07e+00 8.73e-01 2.16e+01 angle pdb=" CA THR A 218 " pdb=" C THR A 218 " pdb=" O THR A 218 " ideal model delta sigma weight residual 121.14 116.46 4.68 1.03e+00 9.43e-01 2.07e+01 angle pdb=" CA ASN A 104 " pdb=" C ASN A 104 " pdb=" O ASN A 104 " ideal model delta sigma weight residual 120.42 115.93 4.49 1.06e+00 8.90e-01 1.79e+01 angle pdb=" C CYS A 217 " pdb=" CA CYS A 217 " pdb=" CB CYS A 217 " ideal model delta sigma weight residual 110.62 116.85 -6.23 1.51e+00 4.39e-01 1.70e+01 ... (remaining 3526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.04: 1410 22.04 - 44.07: 47 44.07 - 66.11: 3 66.11 - 88.14: 0 88.14 - 110.18: 3 Dihedral angle restraints: 1463 sinusoidal: 434 harmonic: 1029 Sorted by residual: dihedral pdb=" C7 NG0 A 900 " pdb=" C8 NG0 A 900 " pdb=" C9 NG0 A 900 " pdb=" N1 NG0 A 900 " ideal model delta sinusoidal sigma weight residual -53.63 56.55 -110.18 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C11 NG0 A 900 " pdb=" C10 NG0 A 900 " pdb=" N1 NG0 A 900 " pdb=" C9 NG0 A 900 " ideal model delta sinusoidal sigma weight residual -55.08 53.24 -108.32 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C10 NG0 A 900 " pdb=" C9 NG0 A 900 " pdb=" N1 NG0 A 900 " pdb=" C8 NG0 A 900 " ideal model delta sinusoidal sigma weight residual -53.68 53.31 -106.99 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 1460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 295 0.051 - 0.103: 109 0.103 - 0.154: 27 0.154 - 0.205: 5 0.205 - 0.256: 1 Chirality restraints: 437 Sorted by residual: chirality pdb=" CA TYR A 252 " pdb=" N TYR A 252 " pdb=" C TYR A 252 " pdb=" CB TYR A 252 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA THR A 101 " pdb=" N THR A 101 " pdb=" C THR A 101 " pdb=" CB THR A 101 " both_signs ideal model delta sigma weight residual False 2.53 2.72 -0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 434 not shown) Planarity restraints: 431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 114 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C ASP A 114 " 0.038 2.00e-02 2.50e+03 pdb=" O ASP A 114 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 115 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 216 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.79e+00 pdb=" C ASP A 216 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP A 216 " 0.014 2.00e-02 2.50e+03 pdb=" N CYS A 217 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 165 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C ARG A 165 " 0.035 2.00e-02 2.50e+03 pdb=" O ARG A 165 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR A 166 " -0.012 2.00e-02 2.50e+03 ... (remaining 428 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 391 2.76 - 3.29: 2444 3.29 - 3.83: 4109 3.83 - 4.36: 4500 4.36 - 4.90: 7882 Nonbonded interactions: 19326 Sorted by model distance: nonbonded pdb=" O ASP A 147 " pdb=" O HOH A1001 " model vdw 2.222 2.440 nonbonded pdb=" O PRO A 122 " pdb=" OG SER A 125 " model vdw 2.446 2.440 nonbonded pdb=" O HIS A 171 " pdb=" N ALA A 175 " model vdw 2.453 2.520 nonbonded pdb=" N THR A 101 " pdb=" O THR A 101 " model vdw 2.481 2.496 nonbonded pdb=" NH1 ARG A 276 " pdb=" O ILE D 488 " model vdw 2.539 2.520 ... (remaining 19321 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 1658 2.51 5 N 409 2.21 5 O 435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.090 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.030 Process input model: 12.360 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Set scattering table: 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:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 0.149 2574 Z= 0.676 Angle : 1.078 14.945 3531 Z= 0.670 Chirality : 0.056 0.256 437 Planarity : 0.007 0.046 431 Dihedral : 12.506 110.177 790 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.41), residues: 337 helix: 1.37 (0.32), residues: 227 sheet: 0.80 (0.87), residues: 24 loop : -1.08 (0.57), residues: 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.293 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.6100 time to fit residues: 29.5311 Evaluate side-chains 30 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 7.9990 chunk 25 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN A 127 ASN A 150 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 2574 Z= 0.207 Angle : 0.595 7.919 3531 Z= 0.318 Chirality : 0.041 0.141 437 Planarity : 0.004 0.035 431 Dihedral : 10.302 98.578 373 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.43), residues: 337 helix: 2.18 (0.32), residues: 227 sheet: 0.26 (0.94), residues: 24 loop : -1.46 (0.57), residues: 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.303 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 33 average time/residue: 0.7491 time to fit residues: 25.8846 Evaluate side-chains 29 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.306 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0781 time to fit residues: 0.5021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.0270 chunk 33 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 2574 Z= 0.175 Angle : 0.544 8.697 3531 Z= 0.285 Chirality : 0.039 0.136 437 Planarity : 0.004 0.031 431 Dihedral : 10.214 97.504 373 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.43), residues: 337 helix: 2.56 (0.32), residues: 228 sheet: 0.34 (0.90), residues: 24 loop : -1.58 (0.57), residues: 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.248 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 33 average time/residue: 0.6380 time to fit residues: 22.1183 Evaluate side-chains 30 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.297 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.3955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 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: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 2574 Z= 0.224 Angle : 0.576 9.008 3531 Z= 0.301 Chirality : 0.041 0.137 437 Planarity : 0.004 0.031 431 Dihedral : 10.530 98.247 373 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.43), residues: 337 helix: 2.36 (0.32), residues: 228 sheet: 0.61 (0.95), residues: 24 loop : -1.62 (0.57), residues: 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.318 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 32 average time/residue: 0.8330 time to fit residues: 27.8723 Evaluate side-chains 28 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.343 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 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: 0.8053 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 2574 Z= 0.227 Angle : 0.578 9.258 3531 Z= 0.301 Chirality : 0.041 0.133 437 Planarity : 0.004 0.032 431 Dihedral : 10.650 98.249 373 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 3.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.43), residues: 337 helix: 2.24 (0.32), residues: 228 sheet: 0.54 (1.02), residues: 24 loop : -1.66 (0.56), residues: 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.259 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 32 average time/residue: 0.7624 time to fit residues: 25.4482 Evaluate side-chains 30 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.288 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.0917 time to fit residues: 1.5055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 10 optimal weight: 0.0670 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 2574 Z= 0.155 Angle : 0.523 9.430 3531 Z= 0.267 Chirality : 0.039 0.131 437 Planarity : 0.004 0.031 431 Dihedral : 10.390 97.325 373 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.44), residues: 337 helix: 2.61 (0.32), residues: 228 sheet: 0.64 (1.05), residues: 24 loop : -1.65 (0.54), residues: 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.258 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 32 average time/residue: 0.6776 time to fit residues: 22.7936 Evaluate side-chains 29 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.305 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.8025 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 2574 Z= 0.194 Angle : 0.554 9.595 3531 Z= 0.283 Chirality : 0.040 0.132 437 Planarity : 0.004 0.030 431 Dihedral : 10.494 97.788 373 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.44), residues: 337 helix: 2.46 (0.32), residues: 228 sheet: 0.66 (1.08), residues: 24 loop : -1.61 (0.54), residues: 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.298 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 29 average time/residue: 0.7351 time to fit residues: 22.3832 Evaluate side-chains 28 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.300 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.3985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 0.0060 chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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: 0.8006 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2574 Z= 0.176 Angle : 0.538 9.795 3531 Z= 0.274 Chirality : 0.039 0.131 437 Planarity : 0.004 0.030 431 Dihedral : 10.438 97.504 373 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.44), residues: 337 helix: 2.52 (0.32), residues: 228 sheet: 0.81 (1.09), residues: 24 loop : -1.63 (0.55), residues: 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.295 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 31 average time/residue: 0.6951 time to fit residues: 22.6664 Evaluate side-chains 28 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.294 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8042 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 2574 Z= 0.208 Angle : 0.566 9.910 3531 Z= 0.289 Chirality : 0.040 0.132 437 Planarity : 0.004 0.029 431 Dihedral : 10.558 97.961 373 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.44), residues: 337 helix: 2.36 (0.32), residues: 228 sheet: 0.62 (1.06), residues: 24 loop : -1.64 (0.56), residues: 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.303 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 29 average time/residue: 0.8822 time to fit residues: 26.6802 Evaluate side-chains 29 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.296 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.3991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8079 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 2574 Z= 0.256 Angle : 0.605 9.965 3531 Z= 0.311 Chirality : 0.041 0.133 437 Planarity : 0.004 0.028 431 Dihedral : 10.736 98.317 373 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.43), residues: 337 helix: 2.10 (0.32), residues: 228 sheet: 0.38 (1.03), residues: 24 loop : -1.78 (0.54), residues: 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.313 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 31 average time/residue: 0.7920 time to fit residues: 25.6982 Evaluate side-chains 31 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.3910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.0670 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 0.0980 chunk 33 optimal weight: 0.6980 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.160280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143388 restraints weight = 3315.427| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.74 r_work: 0.3683 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 1.56 restraints_weight: 0.2500 r_work: 0.3662 rms_B_bonded: 1.64 restraints_weight: 0.1250 r_work: 0.3649 rms_B_bonded: 1.79 restraints_weight: 0.0625 r_work: 0.3635 rms_B_bonded: 2.00 restraints_weight: 0.0312 r_work: 0.3618 rms_B_bonded: 2.27 restraints_weight: 0.0156 r_work: 0.3599 rms_B_bonded: 2.63 restraints_weight: 0.0078 r_work: 0.3578 rms_B_bonded: 3.07 restraints_weight: 0.0039 r_work: 0.3553 rms_B_bonded: 3.62 restraints_weight: 0.0020 r_work: 0.3524 rms_B_bonded: 4.31 restraints_weight: 0.0010 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 2574 Z= 0.155 Angle : 0.528 10.123 3531 Z= 0.268 Chirality : 0.039 0.130 437 Planarity : 0.004 0.030 431 Dihedral : 10.434 97.455 373 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.45), residues: 337 helix: 2.51 (0.32), residues: 233 sheet: 0.55 (1.04), residues: 24 loop : -1.80 (0.57), residues: 80 =============================================================================== Job complete usr+sys time: 1161.44 seconds wall clock time: 22 minutes 6.88 seconds (1326.88 seconds total)