Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 22:44:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/08_2023/8ero_28556_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/08_2023/8ero_28556.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/08_2023/8ero_28556_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/08_2023/8ero_28556_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/08_2023/8ero_28556_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/08_2023/8ero_28556.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/08_2023/8ero_28556.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/08_2023/8ero_28556_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ero_28556/08_2023/8ero_28556_updated.pdb" } resolution = 3.2 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= 0.006 sd= 0.191 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 50 5.16 5 C 4156 2.51 5 N 892 2.21 5 O 1044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 6154 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2836 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 15, 'TRANS': 348} Chain: "B" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2836 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 15, 'TRANS': 348} Chain: "A" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 241 Unusual residues: {' MG': 2, 'CDP': 1, 'LBN': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 462 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'LBN:plan-2': 11, 'LBN:plan-3': 12, 'LBN:plan-1': 11} Unresolved non-hydrogen planarities: 116 Chain: "B" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 241 Unusual residues: {' MG': 2, 'CDP': 1, 'LBN': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 462 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'LBN:plan-2': 11, 'LBN:plan-3': 12, 'LBN:plan-1': 11} Unresolved non-hydrogen planarities: 116 Time building chain proxies: 3.86, per 1000 atoms: 0.63 Number of scatterers: 6154 At special positions: 0 Unit cell: (78.1, 122.1, 70.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 8 15.00 Mg 4 11.99 O 1044 8.00 N 892 7.00 C 4156 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: 2.21 Conformation dependent library (CDL) restraints added in 987.3 milliseconds 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 2 sheets defined 71.2% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 23 through 29 Processing helix chain 'A' and resid 41 through 56 Proline residue: A 44 - end of helix Processing helix chain 'A' and resid 63 through 88 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 94 through 119 Processing helix chain 'A' and resid 126 through 151 removed outlier: 3.550A pdb=" N MET A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 161 through 180 Processing helix chain 'A' and resid 191 through 208 Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.953A pdb=" N TRP A 213 " --> pdb=" O PRO A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 248 Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 266 through 284 removed outlier: 3.705A pdb=" N HIS A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 284 " --> pdb=" O MET A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 292 No H-bonds generated for 'chain 'A' and resid 289 through 292' Processing helix chain 'A' and resid 294 through 317 Processing helix chain 'A' and resid 330 through 340 Processing helix chain 'A' and resid 349 through 377 Processing helix chain 'B' and resid 23 through 29 Processing helix chain 'B' and resid 41 through 56 Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 63 through 88 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 94 through 119 Processing helix chain 'B' and resid 126 through 151 removed outlier: 3.550A pdb=" N MET B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 161 through 180 Processing helix chain 'B' and resid 191 through 208 Processing helix chain 'B' and resid 210 through 214 removed outlier: 3.953A pdb=" N TRP B 213 " --> pdb=" O PRO B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 248 Proline residue: B 228 - end of helix Processing helix chain 'B' and resid 266 through 284 removed outlier: 3.705A pdb=" N HIS B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 284 " --> pdb=" O MET B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 292 No H-bonds generated for 'chain 'B' and resid 289 through 292' Processing helix chain 'B' and resid 294 through 317 Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 349 through 377 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 38 removed outlier: 5.825A pdb=" N LEU A 184 " --> pdb=" O SER A 37 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 36 through 38 removed outlier: 5.825A pdb=" N LEU B 184 " --> pdb=" O SER B 37 " (cutoff:3.500A) No H-bonds generated for sheet with id= B 378 hydrogen bonds defined for protein. 954 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: 1.64 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 892 1.32 - 1.44: 1631 1.44 - 1.56: 3663 1.56 - 1.69: 14 1.69 - 1.81: 74 Bond restraints: 6274 Sorted by residual: bond pdb=" C3' CDP A 513 " pdb=" C4' CDP A 513 " ideal model delta sigma weight residual 1.305 1.521 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C3' CDP B 516 " pdb=" C4' CDP B 516 " ideal model delta sigma weight residual 1.305 1.521 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C4' CDP A 513 " pdb=" O4' CDP A 513 " ideal model delta sigma weight residual 1.615 1.442 0.173 2.00e-02 2.50e+03 7.51e+01 bond pdb=" C4' CDP B 516 " pdb=" O4' CDP B 516 " ideal model delta sigma weight residual 1.615 1.442 0.173 2.00e-02 2.50e+03 7.51e+01 bond pdb=" O2 LBN B 515 " pdb=" P1 LBN B 515 " ideal model delta sigma weight residual 1.650 1.482 0.168 2.00e-02 2.50e+03 7.07e+01 ... (remaining 6269 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.91: 154 105.91 - 112.93: 3303 112.93 - 119.94: 2294 119.94 - 126.95: 2584 126.95 - 133.97: 81 Bond angle restraints: 8416 Sorted by residual: angle pdb=" O1 LBN B 515 " pdb=" P1 LBN B 515 " pdb=" O2 LBN B 515 " ideal model delta sigma weight residual 93.45 109.04 -15.59 3.00e+00 1.11e-01 2.70e+01 angle pdb=" O1 LBN A 512 " pdb=" P1 LBN A 512 " pdb=" O2 LBN A 512 " ideal model delta sigma weight residual 93.45 109.04 -15.59 3.00e+00 1.11e-01 2.70e+01 angle pdb=" O3 LBN A 512 " pdb=" P1 LBN A 512 " pdb=" O4 LBN A 512 " ideal model delta sigma weight residual 119.36 107.44 11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O3 LBN B 515 " pdb=" P1 LBN B 515 " pdb=" O4 LBN B 515 " ideal model delta sigma weight residual 119.36 107.44 11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O1 LBN B 507 " pdb=" P1 LBN B 507 " pdb=" O2 LBN B 507 " ideal model delta sigma weight residual 93.45 104.29 -10.84 3.00e+00 1.11e-01 1.31e+01 ... (remaining 8411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.32: 3460 26.32 - 52.65: 170 52.65 - 78.97: 30 78.97 - 105.29: 4 105.29 - 131.62: 22 Dihedral angle restraints: 3686 sinusoidal: 1584 harmonic: 2102 Sorted by residual: dihedral pdb=" C32 LBN A 509 " pdb=" C33 LBN A 509 " pdb=" C4 LBN A 509 " pdb=" C7 LBN A 509 " ideal model delta sinusoidal sigma weight residual 179.89 -48.49 -131.62 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C32 LBN B 512 " pdb=" C33 LBN B 512 " pdb=" C4 LBN B 512 " pdb=" C7 LBN B 512 " ideal model delta sinusoidal sigma weight residual 179.89 -48.49 -131.62 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C32 LBN A 506 " pdb=" C33 LBN A 506 " pdb=" C4 LBN A 506 " pdb=" C7 LBN A 506 " ideal model delta sinusoidal sigma weight residual 179.89 55.90 123.99 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 3683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 738 0.049 - 0.098: 176 0.098 - 0.147: 32 0.147 - 0.196: 0 0.196 - 0.246: 4 Chirality restraints: 950 Sorted by residual: chirality pdb=" C3' CDP A 513 " pdb=" C2' CDP A 513 " pdb=" C4' CDP A 513 " pdb=" O3' CDP A 513 " both_signs ideal model delta sigma weight residual False -2.39 -2.64 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C3' CDP B 516 " pdb=" C2' CDP B 516 " pdb=" C4' CDP B 516 " pdb=" O3' CDP B 516 " both_signs ideal model delta sigma weight residual False -2.39 -2.64 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C2 LBN A 504 " pdb=" C1 LBN A 504 " pdb=" C3 LBN A 504 " pdb=" O7 LBN A 504 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 947 not shown) Planarity restraints: 972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN B 507 " -0.230 2.00e-02 2.50e+03 2.29e-01 5.26e+02 pdb=" C42 LBN B 507 " 0.234 2.00e-02 2.50e+03 pdb=" C5 LBN B 507 " 0.225 2.00e-02 2.50e+03 pdb=" C8 LBN B 507 " -0.228 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN A 504 " 0.230 2.00e-02 2.50e+03 2.29e-01 5.26e+02 pdb=" C42 LBN A 504 " -0.234 2.00e-02 2.50e+03 pdb=" C5 LBN A 504 " -0.225 2.00e-02 2.50e+03 pdb=" C8 LBN A 504 " 0.228 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 238 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C TYR A 238 " 0.031 2.00e-02 2.50e+03 pdb=" O TYR A 238 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 239 " -0.011 2.00e-02 2.50e+03 ... (remaining 969 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 50 2.59 - 3.17: 5235 3.17 - 3.74: 8782 3.74 - 4.32: 11684 4.32 - 4.90: 20344 Nonbonded interactions: 46095 Sorted by model distance: nonbonded pdb=" OD1 ASP A 132 " pdb="MG MG A 501 " model vdw 2.011 2.170 nonbonded pdb=" OD1 ASP B 132 " pdb="MG MG B 504 " model vdw 2.011 2.170 nonbonded pdb="MG MG B 505 " pdb=" O1A CDP B 516 " model vdw 2.024 2.170 nonbonded pdb="MG MG A 502 " pdb=" O1A CDP A 513 " model vdw 2.024 2.170 nonbonded pdb=" OD1 ASP A 136 " pdb="MG MG A 501 " model vdw 2.060 2.170 ... (remaining 46090 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 383 or resid 503 or (resid 506 and (name C10 or \ name C13 or name C16 or name C29 or name C30 or name C31 or name C32 or name C3 \ 3 or name C4 or name C7 )) or (resid 507 and (name C26 or name C27 or name C28 o \ r name C29 or name C30 or name C31 or name C32)) or resid 508 through 509 or (re \ sid 510 and (name C10 or name C13 or name C26 or name C27 or name C28 or name C2 \ 9 or name C30 or name C31 or name C32 or name C33 or name C4 or name C7 )) or re \ sid 511 or (resid 512 and (name C25 or name C26 or name C27 or name C28 or name \ C29 or name C30 or name C31 or name C32)) or resid 514 or (resid 515 and (name C \ 25 or name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or na \ me C32)))) selection = (chain 'B' and (resid 20 through 383 or (resid 503 and (name C10 or name C13 or \ name C16 or name C29 or name C30 or name C31 or name C32 or name C33 or name C4 \ or name C7 )) or resid 506 or (resid 507 and (name C26 or name C27 or name C28 o \ r name C29 or name C30 or name C31 or name C32)) or resid 508 through 511 or (re \ sid 512 and (name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ 0 or name C31 or name C32)) or (resid 514 and (name C10 or name C13 or name C26 \ or name C27 or name C28 or name C29 or name C30 or name C31 or name C32 or name \ C33 or name C4 or name C7 )) or (resid 515 and (name C25 or name C26 or name C27 \ or name C28 or name C29 or name C30 or name C31 or name C32)))) } 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 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: 0.380 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: 2.290 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 20.250 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 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 0.216 6274 Z= 0.509 Angle : 0.855 15.587 8416 Z= 0.402 Chirality : 0.044 0.246 950 Planarity : 0.012 0.229 972 Dihedral : 19.234 131.617 2342 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % 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: 0.41 (0.32), residues: 724 helix: 1.78 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -2.81 (0.38), residues: 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.587 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1764 time to fit residues: 24.2706 Evaluate side-chains 78 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.628 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.0270 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 242 ASN B 25 GLN B 74 ASN B 242 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 6274 Z= 0.203 Angle : 0.598 5.819 8416 Z= 0.322 Chirality : 0.041 0.151 950 Planarity : 0.006 0.041 972 Dihedral : 18.250 128.177 1084 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.32), residues: 724 helix: 1.82 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -2.88 (0.38), residues: 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.675 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 84 average time/residue: 0.1695 time to fit residues: 19.7014 Evaluate side-chains 80 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.662 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0669 time to fit residues: 1.8472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 242 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 242 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 6274 Z= 0.256 Angle : 0.640 6.106 8416 Z= 0.345 Chirality : 0.042 0.168 950 Planarity : 0.006 0.040 972 Dihedral : 16.029 119.637 1084 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.31), residues: 724 helix: 1.42 (0.23), residues: 480 sheet: None (None), residues: 0 loop : -2.54 (0.39), residues: 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.659 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 92 average time/residue: 0.1470 time to fit residues: 19.2085 Evaluate side-chains 84 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0620 time to fit residues: 1.7539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.0030 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 144 ASN A 242 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 242 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6274 Z= 0.217 Angle : 0.609 6.489 8416 Z= 0.329 Chirality : 0.040 0.167 950 Planarity : 0.005 0.041 972 Dihedral : 14.892 115.278 1084 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.31), residues: 724 helix: 1.45 (0.23), residues: 478 sheet: None (None), residues: 0 loop : -2.57 (0.39), residues: 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.634 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 87 average time/residue: 0.1491 time to fit residues: 18.2538 Evaluate side-chains 78 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.714 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0834 time to fit residues: 1.3994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 6274 Z= 0.278 Angle : 0.660 9.071 8416 Z= 0.355 Chirality : 0.042 0.175 950 Planarity : 0.006 0.040 972 Dihedral : 14.527 109.158 1084 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.31), residues: 724 helix: 1.19 (0.23), residues: 484 sheet: -1.31 (0.98), residues: 24 loop : -2.77 (0.41), residues: 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.677 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 91 average time/residue: 0.1480 time to fit residues: 18.9997 Evaluate side-chains 83 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.585 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0539 time to fit residues: 1.0119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN B 175 GLN B 372 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6274 Z= 0.203 Angle : 0.606 8.452 8416 Z= 0.328 Chirality : 0.040 0.162 950 Planarity : 0.005 0.040 972 Dihedral : 13.716 106.281 1084 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.31), residues: 724 helix: 1.34 (0.23), residues: 484 sheet: -1.27 (1.01), residues: 24 loop : -2.72 (0.41), residues: 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.635 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 85 average time/residue: 0.1448 time to fit residues: 17.4474 Evaluate side-chains 81 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.576 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- 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: 0.7183 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 6274 Z= 0.257 Angle : 0.651 8.229 8416 Z= 0.348 Chirality : 0.041 0.185 950 Planarity : 0.005 0.041 972 Dihedral : 13.692 101.747 1084 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.31), residues: 724 helix: 1.21 (0.23), residues: 484 sheet: -1.42 (0.98), residues: 24 loop : -2.69 (0.41), residues: 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.651 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 79 average time/residue: 0.1537 time to fit residues: 17.0457 Evaluate side-chains 75 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.641 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6274 Z= 0.226 Angle : 0.618 7.095 8416 Z= 0.333 Chirality : 0.040 0.165 950 Planarity : 0.005 0.042 972 Dihedral : 13.372 98.059 1084 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.31), residues: 724 helix: 1.22 (0.23), residues: 484 sheet: -1.43 (0.99), residues: 24 loop : -2.62 (0.41), residues: 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.644 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 84 average time/residue: 0.1521 time to fit residues: 18.0173 Evaluate side-chains 84 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0771 time to fit residues: 1.5506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 0.2980 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 6274 Z= 0.168 Angle : 0.583 9.205 8416 Z= 0.313 Chirality : 0.039 0.143 950 Planarity : 0.005 0.042 972 Dihedral : 12.621 93.574 1084 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.32), residues: 724 helix: 1.59 (0.23), residues: 470 sheet: -1.15 (1.06), residues: 24 loop : -2.90 (0.40), residues: 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.670 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 88 average time/residue: 0.1620 time to fit residues: 19.6752 Evaluate side-chains 82 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.661 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0600 time to fit residues: 1.0261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.033 6274 Z= 0.446 Angle : 0.776 10.958 8416 Z= 0.408 Chirality : 0.046 0.206 950 Planarity : 0.006 0.040 972 Dihedral : 13.643 88.863 1084 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.30), residues: 724 helix: 0.86 (0.23), residues: 482 sheet: None (None), residues: 0 loop : -2.87 (0.36), residues: 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.647 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 78 average time/residue: 0.1363 time to fit residues: 15.6911 Evaluate side-chains 76 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.627 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0840 time to fit residues: 1.4510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.180083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144300 restraints weight = 6447.414| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.47 r_work: 0.3373 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6274 Z= 0.226 Angle : 0.642 7.383 8416 Z= 0.346 Chirality : 0.041 0.168 950 Planarity : 0.005 0.041 972 Dihedral : 13.217 88.276 1084 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.31), residues: 724 helix: 1.06 (0.23), residues: 484 sheet: -1.67 (0.92), residues: 24 loop : -2.71 (0.40), residues: 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1294.42 seconds wall clock time: 24 minutes 18.99 seconds (1458.99 seconds total)