Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 05:05:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0q_26948/04_2023/7v0q_26948.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0q_26948/04_2023/7v0q_26948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0q_26948/04_2023/7v0q_26948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0q_26948/04_2023/7v0q_26948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0q_26948/04_2023/7v0q_26948.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0q_26948/04_2023/7v0q_26948.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.249 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 3282 2.51 5 N 916 2.21 5 O 1080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X ASP 11": "OD1" <-> "OD2" Residue "X ASP 111": "OD1" <-> "OD2" Residue "X GLU 310": "OE1" <-> "OE2" Residue "X GLU 439": "OE1" <-> "OE2" Residue "X ASP 490": "OD1" <-> "OD2" Residue "X GLU 599": "OE1" <-> "OE2" Residue "X ASP 620": "OD1" <-> "OD2" Residue "X GLU 634": "OE1" <-> "OE2" Residue "X PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 5301 Number of models: 1 Model: "" Number of chains: 1 Chain: "X" Number of atoms: 5301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5301 Inner-chain residues flagged as termini: ['pdbres="ALA X 691 "'] Classifications: {'peptide': 658, 'water': 127} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 627, None: 127} Not linked: pdbres="ALA X 691 " pdbres="HOH X 701 " Not linked: pdbres="HOH X 701 " pdbres="HOH X 702 " Not linked: pdbres="HOH X 702 " pdbres="HOH X 703 " Not linked: pdbres="HOH X 703 " pdbres="HOH X 704 " Not linked: pdbres="HOH X 704 " pdbres="HOH X 705 " ... (remaining 122 not shown) Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 3.40, per 1000 atoms: 0.64 Number of scatterers: 5301 At special positions: 0 Unit cell: (98.355, 101.675, 73.04, 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 23 16.00 O 1080 8.00 N 916 7.00 C 3282 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: 2.08 Conformation dependent library (CDL) restraints added in 983.5 milliseconds 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1234 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 10 sheets defined 21.3% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'X' and resid 13 through 21 Processing helix chain 'X' and resid 51 through 58 removed outlier: 3.570A pdb=" N ALA X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 151 through 159 Processing helix chain 'X' and resid 187 through 197 Processing helix chain 'X' and resid 201 through 206 removed outlier: 4.047A pdb=" N SER X 206 " --> pdb=" O GLU X 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 227 Processing helix chain 'X' and resid 247 through 258 removed outlier: 4.141A pdb=" N ILE X 251 " --> pdb=" O GLY X 247 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 268 Processing helix chain 'X' and resid 269 through 283 removed outlier: 4.344A pdb=" N ALA X 273 " --> pdb=" O TRP X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 368 through 374 Processing helix chain 'X' and resid 381 through 389 removed outlier: 3.661A pdb=" N ILE X 389 " --> pdb=" O LEU X 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 436 removed outlier: 3.914A pdb=" N TYR X 435 " --> pdb=" O ILE X 431 " (cutoff:3.500A) Processing helix chain 'X' and resid 441 through 459 Processing helix chain 'X' and resid 550 through 552 No H-bonds generated for 'chain 'X' and resid 550 through 552' Processing sheet with id=AA1, first strand: chain 'X' and resid 7 through 11 removed outlier: 6.826A pdb=" N TYR X 44 " --> pdb=" O LYS X 8 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS X 10 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE X 42 " --> pdb=" O CYS X 10 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER X 105 " --> pdb=" O VAL X 94 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL X 94 " --> pdb=" O SER X 105 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N THR X 107 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ALA X 92 " --> pdb=" O THR X 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 31 through 34 removed outlier: 4.709A pdb=" N LEU X 31 " --> pdb=" O GLN X 133 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU X 130 " --> pdb=" O LEU X 121 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU X 121 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY X 132 " --> pdb=" O LEU X 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 163 through 169 Processing sheet with id=AA4, first strand: chain 'X' and resid 362 through 367 removed outlier: 3.804A pdb=" N SER X 362 " --> pdb=" O SER X 352 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR X 330 " --> pdb=" O LEU X 349 " (cutoff:3.500A) removed outlier: 11.935A pdb=" N THR X 328 " --> pdb=" O PRO X 351 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE X 326 " --> pdb=" O PHE X 292 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE X 292 " --> pdb=" O PHE X 326 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR X 328 " --> pdb=" O THR X 290 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR X 290 " --> pdb=" O THR X 328 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR X 330 " --> pdb=" O VAL X 288 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL X 288 " --> pdb=" O THR X 330 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS X 332 " --> pdb=" O ALA X 286 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA X 286 " --> pdb=" O CYS X 332 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N VAL X 288 " --> pdb=" O THR X 420 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR X 420 " --> pdb=" O VAL X 288 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR X 290 " --> pdb=" O ILE X 418 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE X 418 " --> pdb=" O THR X 290 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 303 through 309 removed outlier: 5.992A pdb=" N ILE X 304 " --> pdb=" O VAL X 394 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TRP X 396 " --> pdb=" O ILE X 304 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU X 306 " --> pdb=" O TRP X 396 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N CYS X 398 " --> pdb=" O GLU X 306 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR X 308 " --> pdb=" O CYS X 398 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 408 through 409 removed outlier: 6.337A pdb=" N ASP X 408 " --> pdb=" O PHE X 578 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N GLN X 580 " --> pdb=" O ASP X 408 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU X 485 " --> pdb=" O CYS X 586 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'X' and resid 408 through 409 removed outlier: 6.337A pdb=" N ASP X 408 " --> pdb=" O PHE X 578 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N GLN X 580 " --> pdb=" O ASP X 408 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS X 505 " --> pdb=" O THR X 534 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR X 534 " --> pdb=" O LYS X 505 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL X 507 " --> pdb=" O HIS X 532 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N HIS X 532 " --> pdb=" O VAL X 507 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU X 509 " --> pdb=" O LYS X 530 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS X 530 " --> pdb=" O LEU X 509 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE X 511 " --> pdb=" O ARG X 528 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG X 528 " --> pdb=" O ILE X 511 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL X 513 " --> pdb=" O LEU X 526 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 475 through 480 Processing sheet with id=AA9, first strand: chain 'X' and resid 590 through 593 Processing sheet with id=AB1, first strand: chain 'X' and resid 597 through 599 removed outlier: 6.518A pdb=" N ALA X 598 " --> pdb=" O VAL X 685 " (cutoff:3.500A) 201 hydrogen bonds defined for protein. 558 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: 1.92 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1719 1.34 - 1.46: 1130 1.46 - 1.58: 2401 1.58 - 1.70: 0 1.70 - 1.82: 31 Bond restraints: 5281 Sorted by residual: bond pdb=" N GLY X 489 " pdb=" CA GLY X 489 " ideal model delta sigma weight residual 1.449 1.436 0.013 1.45e-02 4.76e+03 8.03e-01 bond pdb=" CA ILE X 81 " pdb=" CB ILE X 81 " ideal model delta sigma weight residual 1.531 1.541 -0.009 1.16e-02 7.43e+03 6.56e-01 bond pdb=" CA SER X 473 " pdb=" C SER X 473 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.10e-02 2.27e+03 6.46e-01 bond pdb=" C ASP X 344 " pdb=" N GLY X 345 " ideal model delta sigma weight residual 1.335 1.329 0.006 7.50e-03 1.78e+04 6.43e-01 bond pdb=" CB GLU X 144 " pdb=" CG GLU X 144 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.31e-01 ... (remaining 5276 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.81: 149 106.81 - 113.61: 2937 113.61 - 120.40: 1808 120.40 - 127.20: 2200 127.20 - 133.99: 72 Bond angle restraints: 7166 Sorted by residual: angle pdb=" N GLY X 345 " pdb=" CA GLY X 345 " pdb=" C GLY X 345 " ideal model delta sigma weight residual 111.21 114.15 -2.94 1.04e+00 9.25e-01 8.01e+00 angle pdb=" CA LEU X 475 " pdb=" CB LEU X 475 " pdb=" CG LEU X 475 " ideal model delta sigma weight residual 116.30 125.43 -9.13 3.50e+00 8.16e-02 6.81e+00 angle pdb=" CB MET X 672 " pdb=" CG MET X 672 " pdb=" SD MET X 672 " ideal model delta sigma weight residual 112.70 119.53 -6.83 3.00e+00 1.11e-01 5.19e+00 angle pdb=" CD ARG X 16 " pdb=" NE ARG X 16 " pdb=" CZ ARG X 16 " ideal model delta sigma weight residual 124.40 127.52 -3.12 1.40e+00 5.10e-01 4.97e+00 angle pdb=" N PRO X 556 " pdb=" CD PRO X 556 " pdb=" CG PRO X 556 " ideal model delta sigma weight residual 103.20 100.01 3.19 1.50e+00 4.44e-01 4.51e+00 ... (remaining 7161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2786 17.85 - 35.69: 252 35.69 - 53.53: 95 53.53 - 71.38: 31 71.38 - 89.22: 17 Dihedral angle restraints: 3181 sinusoidal: 1277 harmonic: 1904 Sorted by residual: dihedral pdb=" CA ILE X 418 " pdb=" C ILE X 418 " pdb=" N SER X 419 " pdb=" CA SER X 419 " ideal model delta harmonic sigma weight residual -180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CG ARG X 16 " pdb=" CD ARG X 16 " pdb=" NE ARG X 16 " pdb=" CZ ARG X 16 " ideal model delta sinusoidal sigma weight residual 90.00 41.19 48.81 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CA LYS X 436 " pdb=" C LYS X 436 " pdb=" N TYR X 437 " pdb=" CA TYR X 437 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 453 0.029 - 0.057: 225 0.057 - 0.086: 78 0.086 - 0.114: 42 0.114 - 0.143: 13 Chirality restraints: 811 Sorted by residual: chirality pdb=" CB THR X 407 " pdb=" CA THR X 407 " pdb=" OG1 THR X 407 " pdb=" CG2 THR X 407 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA ILE X 631 " pdb=" N ILE X 631 " pdb=" C ILE X 631 " pdb=" CB ILE X 631 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CG LEU X 531 " pdb=" CB LEU X 531 " pdb=" CD1 LEU X 531 " pdb=" CD2 LEU X 531 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 808 not shown) Planarity restraints: 923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN X 555 " -0.027 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO X 556 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO X 556 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO X 556 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU X 339 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO X 340 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO X 340 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO X 340 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG X 16 " 0.108 9.50e-02 1.11e+02 4.89e-02 1.87e+00 pdb=" NE ARG X 16 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG X 16 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG X 16 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG X 16 " 0.000 2.00e-02 2.50e+03 ... (remaining 920 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 722 2.76 - 3.30: 4743 3.30 - 3.83: 9669 3.83 - 4.37: 11275 4.37 - 4.90: 19023 Nonbonded interactions: 45432 Sorted by model distance: nonbonded pdb=" OE2 GLU X 331 " pdb=" OH TYR X 435 " model vdw 2.227 2.440 nonbonded pdb=" O PRO X 557 " pdb=" OG1 THR X 560 " model vdw 2.281 2.440 nonbonded pdb=" O LEU X 349 " pdb=" O HOH X 701 " model vdw 2.291 2.440 nonbonded pdb=" O LEU X 160 " pdb=" O HOH X 702 " model vdw 2.292 2.440 nonbonded pdb=" O ARG X 628 " pdb=" O HOH X 703 " model vdw 2.293 2.440 ... (remaining 45427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.570 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 19.260 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 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 : 0.004 0.039 5281 Z= 0.242 Angle : 0.606 9.133 7166 Z= 0.320 Chirality : 0.043 0.143 811 Planarity : 0.005 0.049 923 Dihedral : 18.362 89.222 1947 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.32), residues: 650 helix: 1.96 (0.47), residues: 114 sheet: 1.16 (0.32), residues: 255 loop : 0.80 (0.36), residues: 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.661 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 103 average time/residue: 1.4932 time to fit residues: 159.1049 Evaluate side-chains 100 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.576 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.7939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 70 optimal weight: 50.0000 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 64 GLN X 128 GLN X 175 GLN X 492 GLN X 538 ASN X 600 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.037 5281 Z= 0.397 Angle : 0.633 6.190 7166 Z= 0.332 Chirality : 0.047 0.153 811 Planarity : 0.005 0.041 923 Dihedral : 5.033 17.844 712 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 5.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.32), residues: 650 helix: 2.00 (0.48), residues: 115 sheet: 1.08 (0.31), residues: 254 loop : 0.69 (0.36), residues: 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 95 time to evaluate : 0.566 Fit side-chains outliers start: 31 outliers final: 19 residues processed: 113 average time/residue: 1.5299 time to fit residues: 179.0311 Evaluate side-chains 112 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.607 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 10 residues processed: 9 average time/residue: 0.5146 time to fit residues: 5.8950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 50.0000 chunk 76 optimal weight: 50.0000 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 128 GLN X 492 GLN X 499 ASN ** X 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 5281 Z= 0.250 Angle : 0.543 5.706 7166 Z= 0.284 Chirality : 0.043 0.138 811 Planarity : 0.004 0.033 923 Dihedral : 4.746 17.771 712 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 5.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.32), residues: 650 helix: 2.19 (0.48), residues: 115 sheet: 1.08 (0.31), residues: 252 loop : 0.72 (0.36), residues: 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 92 time to evaluate : 0.641 Fit side-chains outliers start: 31 outliers final: 20 residues processed: 110 average time/residue: 1.4235 time to fit residues: 162.2305 Evaluate side-chains 112 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.566 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 12 residues processed: 8 average time/residue: 0.7508 time to fit residues: 7.2189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 0.0070 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 50.0000 chunk 75 optimal weight: 50.0000 chunk 37 optimal weight: 8.9990 chunk 67 optimal weight: 50.0000 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 overall best weight: 2.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 128 GLN X 492 GLN X 499 ASN ** X 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 5281 Z= 0.213 Angle : 0.516 5.505 7166 Z= 0.268 Chirality : 0.042 0.136 811 Planarity : 0.004 0.032 923 Dihedral : 4.564 17.349 712 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 5.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.32), residues: 650 helix: 2.31 (0.48), residues: 115 sheet: 1.08 (0.31), residues: 252 loop : 0.79 (0.37), residues: 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 0.667 Fit side-chains outliers start: 28 outliers final: 19 residues processed: 109 average time/residue: 1.4545 time to fit residues: 164.2592 Evaluate side-chains 112 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.665 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 12 residues processed: 7 average time/residue: 0.5579 time to fit residues: 5.0738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 67 optimal weight: 50.0000 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 128 GLN X 492 GLN ** X 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 508 GLN ** X 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.046 5281 Z= 0.477 Angle : 0.671 6.389 7166 Z= 0.351 Chirality : 0.049 0.157 811 Planarity : 0.006 0.046 923 Dihedral : 5.193 18.729 712 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 5.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.32), residues: 650 helix: 1.90 (0.48), residues: 115 sheet: 0.99 (0.32), residues: 248 loop : 0.50 (0.36), residues: 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 93 time to evaluate : 0.650 Fit side-chains outliers start: 31 outliers final: 20 residues processed: 110 average time/residue: 1.4759 time to fit residues: 168.0928 Evaluate side-chains 111 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.641 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 12 residues processed: 8 average time/residue: 0.5543 time to fit residues: 5.6544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 75 optimal weight: 50.0000 chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 72 optimal weight: 50.0000 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 68 GLN X 128 GLN X 492 GLN X 499 ASN X 559 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 5281 Z= 0.232 Angle : 0.542 6.450 7166 Z= 0.280 Chirality : 0.043 0.137 811 Planarity : 0.004 0.035 923 Dihedral : 4.708 18.858 712 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 5.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.32), residues: 650 helix: 2.21 (0.48), residues: 115 sheet: 1.10 (0.32), residues: 246 loop : 0.61 (0.36), residues: 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.628 Fit side-chains outliers start: 28 outliers final: 21 residues processed: 109 average time/residue: 1.5211 time to fit residues: 171.6320 Evaluate side-chains 113 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 12 residues processed: 9 average time/residue: 0.6825 time to fit residues: 7.3230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 75 optimal weight: 50.0000 chunk 47 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 314 GLN X 492 GLN X 499 ASN X 508 GLN X 559 ASN X 602 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 5281 Z= 0.282 Angle : 0.569 6.888 7166 Z= 0.294 Chirality : 0.044 0.142 811 Planarity : 0.004 0.037 923 Dihedral : 4.828 19.213 712 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 4.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.32), residues: 650 helix: 2.16 (0.48), residues: 115 sheet: 1.08 (0.32), residues: 246 loop : 0.60 (0.36), residues: 289 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 0.584 Fit side-chains outliers start: 27 outliers final: 18 residues processed: 110 average time/residue: 1.4853 time to fit residues: 169.2406 Evaluate side-chains 110 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.672 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 7 average time/residue: 0.6883 time to fit residues: 6.0695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 68 optimal weight: 50.0000 chunk 72 optimal weight: 50.0000 chunk 65 optimal weight: 0.4980 chunk 70 optimal weight: 50.0000 chunk 42 optimal weight: 1.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 492 GLN X 499 ASN X 559 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 5281 Z= 0.229 Angle : 0.540 7.396 7166 Z= 0.278 Chirality : 0.043 0.137 811 Planarity : 0.004 0.037 923 Dihedral : 4.661 19.420 712 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 3.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.32), residues: 650 helix: 2.27 (0.48), residues: 115 sheet: 1.11 (0.32), residues: 246 loop : 0.68 (0.36), residues: 289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.644 Fit side-chains outliers start: 22 outliers final: 17 residues processed: 107 average time/residue: 1.5430 time to fit residues: 170.7246 Evaluate side-chains 107 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.635 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 5 average time/residue: 0.2841 time to fit residues: 2.5072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 66 optimal weight: 50.0000 chunk 69 optimal weight: 50.0000 chunk 46 optimal weight: 10.0000 chunk 74 optimal weight: 50.0000 chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 overall best weight: 5.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 492 GLN X 508 GLN X 559 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.049 5281 Z= 0.503 Angle : 0.691 8.059 7166 Z= 0.361 Chirality : 0.050 0.159 811 Planarity : 0.006 0.050 923 Dihedral : 5.267 21.076 712 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 4.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.32), residues: 650 helix: 1.91 (0.48), residues: 114 sheet: 0.89 (0.32), residues: 248 loop : 0.45 (0.36), residues: 288 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 0.639 Fit side-chains outliers start: 25 outliers final: 18 residues processed: 105 average time/residue: 1.5143 time to fit residues: 164.5244 Evaluate side-chains 106 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.626 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 6 average time/residue: 0.5900 time to fit residues: 4.6638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 50.0000 chunk 71 optimal weight: 50.0000 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 492 GLN X 499 ASN X 508 GLN X 559 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 5281 Z= 0.180 Angle : 0.522 8.257 7166 Z= 0.268 Chirality : 0.042 0.133 811 Planarity : 0.004 0.035 923 Dihedral : 4.611 20.528 712 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.32), residues: 650 helix: 2.28 (0.48), residues: 115 sheet: 1.06 (0.32), residues: 246 loop : 0.65 (0.36), residues: 289 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.579 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 105 average time/residue: 1.4661 time to fit residues: 159.3448 Evaluate side-chains 102 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 1.1160 time to fit residues: 2.0331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 63 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 50.0000 chunk 41 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 13 GLN X 492 GLN X 559 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.120587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.098519 restraints weight = 4970.831| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.20 r_work: 0.2830 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 5281 Z= 0.218 Angle : 0.538 8.345 7166 Z= 0.276 Chirality : 0.042 0.138 811 Planarity : 0.004 0.039 923 Dihedral : 4.645 20.200 712 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.32), residues: 650 helix: 2.29 (0.48), residues: 115 sheet: 1.09 (0.32), residues: 246 loop : 0.68 (0.36), residues: 289 =============================================================================== Job complete usr+sys time: 2951.57 seconds wall clock time: 52 minutes 41.79 seconds (3161.79 seconds total)