Starting phenix.real_space_refine (version: dev) on Fri Feb 17 20:26:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/02_2023/7li7_23362_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/02_2023/7li7_23362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/02_2023/7li7_23362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/02_2023/7li7_23362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/02_2023/7li7_23362_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li7_23362/02_2023/7li7_23362_updated.pdb" } resolution = 4.1 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 80": "OE1" <-> "OE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A ASP 393": "OD1" <-> "OD2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 21": "OD1" <-> "OD2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C GLU 129": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 6177 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4292 Classifications: {'peptide': 537} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 514} Chain: "B" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 114 Unusual residues: {'CLR': 1, 'D10': 1, 'D12': 3, 'HP6': 5, 'LNK': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Time building chain proxies: 4.28, per 1000 atoms: 0.69 Number of scatterers: 6177 At special positions: 0 Unit cell: (71.928, 73.224, 121.176, 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 34 16.00 O 1082 8.00 N 960 7.00 C 4101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 5 sheets defined 46.8% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 99 through 112 Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 122 through 143 Proline residue: A 131 - end of helix removed outlier: 3.841A pdb=" N GLU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 156 through 189 removed outlier: 3.625A pdb=" N LYS A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY A 160 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN A 177 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR A 178 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 274 through 281 Processing helix chain 'A' and resid 286 through 299 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 357 through 390 Processing helix chain 'A' and resid 404 through 416 removed outlier: 4.052A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 447 removed outlier: 3.836A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 455 through 460 removed outlier: 4.125A pdb=" N LYS A 460 " --> pdb=" O HIS A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 483 removed outlier: 3.708A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 483 " --> pdb=" O VAL A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 495 Processing helix chain 'A' and resid 499 through 513 Processing helix chain 'A' and resid 518 through 529 removed outlier: 4.456A pdb=" N ASP A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 540 No H-bonds generated for 'chain 'A' and resid 537 through 540' Processing helix chain 'A' and resid 544 through 558 removed outlier: 3.768A pdb=" N ILE A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 584 Processing helix chain 'A' and resid 587 through 599 Processing helix chain 'A' and resid 604 through 611 Processing sheet with id= A, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.970A pdb=" N ASP B 76 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 69 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 87 through 92 Processing sheet with id= C, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.515A pdb=" N ALA C 39 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE C 95 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR C 94 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.328A pdb=" N LYS C 127 " --> pdb=" O LEU C 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 109 through 113 removed outlier: 3.550A pdb=" N PHE C 111 " --> pdb=" O PHE C 60 " (cutoff:3.500A) 258 hydrogen bonds defined for protein. 672 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: 1.72 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1814 1.34 - 1.46: 1597 1.46 - 1.58: 2889 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6349 Sorted by residual: bond pdb=" N SER C 48 " pdb=" CA SER C 48 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.90e-02 2.77e+03 1.64e+00 bond pdb=" C GLU C 47 " pdb=" N SER C 48 " ideal model delta sigma weight residual 1.329 1.345 -0.016 1.40e-02 5.10e+03 1.35e+00 bond pdb=" C3 CLR A 710 " pdb=" O1 CLR A 710 " ideal model delta sigma weight residual 1.413 1.393 0.020 2.00e-02 2.50e+03 1.02e+00 bond pdb=" C LEU A 119 " pdb=" N PRO A 120 " ideal model delta sigma weight residual 1.340 1.364 -0.024 2.76e-02 1.31e+03 7.62e-01 bond pdb=" CG PRO C 28 " pdb=" CD PRO C 28 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.70e-02 1.37e+03 7.60e-01 ... (remaining 6344 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.34: 210 107.34 - 114.01: 3529 114.01 - 120.67: 2651 120.67 - 127.34: 2142 127.34 - 134.00: 80 Bond angle restraints: 8612 Sorted by residual: angle pdb=" N TRP A 197 " pdb=" CA TRP A 197 " pdb=" C TRP A 197 " ideal model delta sigma weight residual 114.56 111.00 3.56 1.27e+00 6.20e-01 7.84e+00 angle pdb=" C GLU C 47 " pdb=" N SER C 48 " pdb=" CA SER C 48 " ideal model delta sigma weight residual 123.00 131.08 -8.08 3.00e+00 1.11e-01 7.25e+00 angle pdb=" C13 CLR A 710 " pdb=" C17 CLR A 710 " pdb=" C20 CLR A 710 " ideal model delta sigma weight residual 119.60 112.55 7.05 3.00e+00 1.11e-01 5.52e+00 angle pdb=" C20 CLR A 710 " pdb=" C22 CLR A 710 " pdb=" C23 CLR A 710 " ideal model delta sigma weight residual 115.57 108.76 6.81 3.00e+00 1.11e-01 5.16e+00 angle pdb=" CA GLU C 47 " pdb=" C GLU C 47 " pdb=" N SER C 48 " ideal model delta sigma weight residual 115.49 118.10 -2.61 1.24e+00 6.50e-01 4.42e+00 ... (remaining 8607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3305 17.81 - 35.61: 280 35.61 - 53.42: 32 53.42 - 71.23: 5 71.23 - 89.03: 2 Dihedral angle restraints: 3624 sinusoidal: 1424 harmonic: 2200 Sorted by residual: dihedral pdb=" CB GLU A 453 " pdb=" CG GLU A 453 " pdb=" CD GLU A 453 " pdb=" OE1 GLU A 453 " ideal model delta sinusoidal sigma weight residual 0.00 89.03 -89.03 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 136 " pdb=" CG GLU A 136 " pdb=" CD GLU A 136 " pdb=" OE1 GLU A 136 " ideal model delta sinusoidal sigma weight residual 0.00 -84.87 84.87 1 3.00e+01 1.11e-03 9.71e+00 dihedral pdb=" CA ARG A 596 " pdb=" CB ARG A 596 " pdb=" CG ARG A 596 " pdb=" CD ARG A 596 " ideal model delta sinusoidal sigma weight residual 180.00 122.06 57.94 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 945 0.234 - 0.469: 2 0.469 - 0.703: 0 0.703 - 0.937: 0 0.937 - 1.171: 1 Chirality restraints: 948 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.23 -1.17 2.00e-02 2.50e+03 3.43e+03 chirality pdb=" C14 CLR A 710 " pdb=" C13 CLR A 710 " pdb=" C15 CLR A 710 " pdb=" C8 CLR A 710 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C9 CLR A 710 " pdb=" C10 CLR A 710 " pdb=" C11 CLR A 710 " pdb=" C8 CLR A 710 " both_signs ideal model delta sigma weight residual False -2.45 -2.70 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 945 not shown) Planarity restraints: 1048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 402 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 403 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 403 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 403 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 100 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO C 101 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 101 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 101 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 589 " -0.016 5.00e-02 4.00e+02 2.41e-02 9.26e-01 pdb=" N PRO A 590 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 590 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 590 " -0.014 5.00e-02 4.00e+02 ... (remaining 1045 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1876 2.82 - 3.34: 5871 3.34 - 3.86: 10444 3.86 - 4.38: 11371 4.38 - 4.90: 19576 Nonbonded interactions: 49138 Sorted by model distance: nonbonded pdb=" OH TYR A 110 " pdb=" O VAL A 397 " model vdw 2.297 2.440 nonbonded pdb=" O ASN A 112 " pdb=" NZ LYS A 319 " model vdw 2.304 2.520 nonbonded pdb=" O THR A 600 " pdb=" NE ARG A 607 " model vdw 2.304 2.520 nonbonded pdb=" OD1 ASN A 101 " pdb=" NE2 GLN A 332 " model vdw 2.311 2.520 nonbonded pdb=" O SER A 190 " pdb=" OG SER A 190 " model vdw 2.313 2.440 ... (remaining 49133 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 34 5.16 5 C 4101 2.51 5 N 960 2.21 5 O 1082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.120 Check model and map are aligned: 0.080 Process input model: 20.190 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.050 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 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 : 0.002 0.024 6349 Z= 0.131 Angle : 0.603 8.076 8612 Z= 0.292 Chirality : 0.056 1.171 948 Planarity : 0.003 0.034 1047 Dihedral : 12.192 89.034 2219 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -2.70 (0.27), residues: 759 helix: -0.80 (0.24), residues: 370 sheet: -1.58 (0.54), residues: 81 loop : -3.08 (0.32), residues: 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2219 time to fit residues: 43.3843 Evaluate side-chains 117 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.605 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 58 GLN B 132 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 6349 Z= 0.237 Angle : 0.577 14.508 8612 Z= 0.296 Chirality : 0.040 0.197 948 Planarity : 0.005 0.057 1047 Dihedral : 4.275 36.102 909 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -2.01 (0.29), residues: 759 helix: -0.12 (0.25), residues: 364 sheet: -1.94 (0.49), residues: 91 loop : -2.65 (0.34), residues: 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 139 average time/residue: 0.1891 time to fit residues: 34.5032 Evaluate side-chains 117 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 0.622 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0916 time to fit residues: 0.9912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 46 optimal weight: 0.0030 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.0030 chunk 73 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN C 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6349 Z= 0.171 Angle : 0.535 14.787 8612 Z= 0.267 Chirality : 0.039 0.150 948 Planarity : 0.005 0.063 1047 Dihedral : 4.254 34.505 909 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.80 (0.29), residues: 759 helix: -0.05 (0.26), residues: 363 sheet: -1.74 (0.51), residues: 92 loop : -2.40 (0.34), residues: 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 0.717 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.2001 time to fit residues: 36.9046 Evaluate side-chains 117 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.675 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 0.0470 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN A 223 HIS A 235 HIS ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN C 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 6349 Z= 0.231 Angle : 0.569 14.825 8612 Z= 0.291 Chirality : 0.040 0.156 948 Planarity : 0.005 0.064 1047 Dihedral : 4.591 32.824 909 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.75 (0.29), residues: 759 helix: -0.09 (0.26), residues: 366 sheet: -1.60 (0.51), residues: 96 loop : -2.33 (0.34), residues: 297 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 0.672 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 144 average time/residue: 0.1773 time to fit residues: 33.9872 Evaluate side-chains 116 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.594 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 30.0000 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN A 217 ASN A 223 HIS B 20 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 61 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 6349 Z= 0.322 Angle : 0.649 15.325 8612 Z= 0.332 Chirality : 0.043 0.143 948 Planarity : 0.005 0.053 1047 Dihedral : 5.227 31.273 909 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.85 (0.29), residues: 759 helix: -0.26 (0.26), residues: 364 sheet: -1.56 (0.52), residues: 96 loop : -2.28 (0.34), residues: 299 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 0.677 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 137 average time/residue: 0.1808 time to fit residues: 33.1253 Evaluate side-chains 121 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.667 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 72 optimal weight: 0.0070 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN A 223 HIS B 20 GLN B 58 GLN C 62 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 6349 Z= 0.216 Angle : 0.590 15.800 8612 Z= 0.298 Chirality : 0.041 0.196 948 Planarity : 0.005 0.065 1047 Dihedral : 5.069 30.308 909 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.73 (0.30), residues: 759 helix: -0.19 (0.27), residues: 360 sheet: -1.43 (0.52), residues: 96 loop : -2.17 (0.35), residues: 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 0.698 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 137 average time/residue: 0.1773 time to fit residues: 32.6445 Evaluate side-chains 115 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 0.764 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0964 time to fit residues: 1.1570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 52 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS B 20 GLN C 58 ASN C 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6349 Z= 0.205 Angle : 0.576 15.887 8612 Z= 0.293 Chirality : 0.041 0.174 948 Planarity : 0.005 0.064 1047 Dihedral : 5.028 30.329 909 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.51 (0.30), residues: 759 helix: -0.13 (0.27), residues: 353 sheet: -1.33 (0.53), residues: 96 loop : -1.85 (0.36), residues: 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.768 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.1903 time to fit residues: 35.0389 Evaluate side-chains 112 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.728 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.0170 chunk 45 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN A 223 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN B 58 GLN C 66 GLN C 98 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6349 Z= 0.200 Angle : 0.596 19.583 8612 Z= 0.296 Chirality : 0.040 0.175 948 Planarity : 0.005 0.070 1047 Dihedral : 5.088 30.549 909 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.46 (0.30), residues: 759 helix: -0.05 (0.27), residues: 356 sheet: -1.30 (0.54), residues: 96 loop : -1.91 (0.36), residues: 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 0.624 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.1755 time to fit residues: 30.1705 Evaluate side-chains 109 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.743 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 6349 Z= 0.272 Angle : 0.646 19.308 8612 Z= 0.325 Chirality : 0.042 0.207 948 Planarity : 0.005 0.068 1047 Dihedral : 5.379 30.868 909 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.51 (0.31), residues: 759 helix: -0.11 (0.27), residues: 360 sheet: -1.37 (0.54), residues: 96 loop : -1.89 (0.37), residues: 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.645 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1748 time to fit residues: 31.2962 Evaluate side-chains 117 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.784 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 36 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 18 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN A 223 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN B 58 GLN C 62 GLN C 66 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6349 Z= 0.212 Angle : 0.628 19.645 8612 Z= 0.308 Chirality : 0.042 0.181 948 Planarity : 0.005 0.072 1047 Dihedral : 5.255 31.354 909 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.44 (0.30), residues: 759 helix: -0.03 (0.27), residues: 357 sheet: -1.36 (0.53), residues: 96 loop : -1.87 (0.36), residues: 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.672 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 125 average time/residue: 0.1652 time to fit residues: 28.0916 Evaluate side-chains 109 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.586 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.0030 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 52 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN A 223 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN C 62 GLN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.192330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.185436 restraints weight = 7517.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.162100 restraints weight = 11743.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.161336 restraints weight = 12254.586| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 6349 Z= 0.193 Angle : 0.623 19.592 8612 Z= 0.308 Chirality : 0.041 0.169 948 Planarity : 0.005 0.071 1047 Dihedral : 5.211 31.373 909 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.48 (0.30), residues: 759 helix: -0.14 (0.27), residues: 365 sheet: -1.33 (0.53), residues: 96 loop : -1.85 (0.36), residues: 298 =============================================================================== Job complete usr+sys time: 1754.58 seconds wall clock time: 32 minutes 46.72 seconds (1966.72 seconds total)