Starting phenix.real_space_refine (version: dev) on Fri Feb 17 20:20:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/02_2023/7li8_23363_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/02_2023/7li8_23363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/02_2023/7li8_23363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/02_2023/7li8_23363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/02_2023/7li8_23363_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/02_2023/7li8_23363_updated.pdb" } resolution = 3.9 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= 0.025 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 ARG 79": "NH1" <-> "NH2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A ARG 538": "NH1" <-> "NH2" 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: 6181 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4303 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 515} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} 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: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 109 Unusual residues: {'D10': 1, 'D12': 3, 'HP6': 6, 'LNK': 1, 'R16': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 4.32, per 1000 atoms: 0.70 Number of scatterers: 6181 At special positions: 0 Unit cell: (68.688, 77.112, 122.472, 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 1081 8.00 N 962 7.00 C 4104 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: 2.60 Conformation dependent library (CDL) restraints added in 1.0 seconds 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 4 sheets defined 43.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 99 through 102 No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.803A pdb=" N PHE A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.628A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 300 removed outlier: 4.556A pdb=" N PHE A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Proline residue: A 288 - end of helix removed outlier: 4.317A pdb=" N SER A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 325 through 337 removed outlier: 4.344A pdb=" N LEU A 337 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 360 through 388 removed outlier: 3.988A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 403 through 416 removed outlier: 3.750A pdb=" N LEU A 406 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 407 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A 408 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 416 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 447 removed outlier: 4.117A pdb=" N ALA A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 486 through 492 removed outlier: 4.382A pdb=" N LEU A 491 " --> pdb=" O TYR A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 514 Processing helix chain 'A' and resid 518 through 529 Processing helix chain 'A' and resid 535 through 557 removed outlier: 3.729A pdb=" N TRP A 541 " --> pdb=" O TRP A 537 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Proline residue: A 546 - end of helix Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.732A pdb=" N ILE A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 597 Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing sheet with id= A, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.633A pdb=" N GLN B 24 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 42 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B 100 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 111 through 113 removed outlier: 3.605A pdb=" N ILE B 70 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY B 68 " --> pdb=" O TRP B 55 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LYS B 57 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N TRP B 66 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG B 59 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 64 " --> pdb=" O ARG B 59 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 109 through 114 removed outlier: 3.730A pdb=" N PHE C 111 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE C 60 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLN C 61 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU C 70 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 87 through 90 removed outlier: 3.561A pdb=" N SER C 89 " --> pdb=" O SER C 96 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 591 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: 1.62 Time building geometry restraints manager: 2.73 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: 1811 1.34 - 1.46: 1452 1.46 - 1.58: 3037 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6349 Sorted by residual: bond pdb=" C7 NAG D 1 " pdb=" N2 NAG D 1 " ideal model delta sigma weight residual 1.337 1.351 -0.014 1.10e-02 8.26e+03 1.52e+00 bond pdb=" CA LEU A 237 " pdb=" CB LEU A 237 " ideal model delta sigma weight residual 1.527 1.553 -0.026 2.48e-02 1.63e+03 1.10e+00 bond pdb=" C2 NAG D 1 " pdb=" N2 NAG D 1 " ideal model delta sigma weight residual 1.454 1.464 -0.010 1.00e-02 1.00e+04 9.91e-01 bond pdb=" CA ILE C 22 " pdb=" CB ILE C 22 " ideal model delta sigma weight residual 1.530 1.540 -0.009 1.05e-02 9.07e+03 7.93e-01 bond pdb=" C1 NAG D 1 " pdb=" C2 NAG D 1 " ideal model delta sigma weight residual 1.526 1.541 -0.015 2.00e-02 2.50e+03 5.62e-01 ... (remaining 6344 not shown) Histogram of bond angle deviations from ideal: 100.86 - 107.49: 231 107.49 - 114.11: 3541 114.11 - 120.74: 2686 120.74 - 127.36: 2056 127.36 - 133.99: 82 Bond angle restraints: 8596 Sorted by residual: angle pdb=" C2 NAG D 1 " pdb=" N2 NAG D 1 " pdb=" C7 NAG D 1 " ideal model delta sigma weight residual 123.12 129.01 -5.89 1.28e+00 6.08e-01 2.11e+01 angle pdb=" N VAL A 102 " pdb=" CA VAL A 102 " pdb=" C VAL A 102 " ideal model delta sigma weight residual 113.53 109.27 4.26 9.80e-01 1.04e+00 1.89e+01 angle pdb=" N VAL A 92 " pdb=" CA VAL A 92 " pdb=" C VAL A 92 " ideal model delta sigma weight residual 113.71 110.54 3.17 9.50e-01 1.11e+00 1.11e+01 angle pdb=" N VAL A 446 " pdb=" CA VAL A 446 " pdb=" C VAL A 446 " ideal model delta sigma weight residual 112.96 109.70 3.26 1.00e+00 1.00e+00 1.07e+01 angle pdb=" C GLY B 121 " pdb=" N SER B 122 " pdb=" CA SER B 122 " ideal model delta sigma weight residual 120.38 124.54 -4.16 1.37e+00 5.33e-01 9.22e+00 ... (remaining 8591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.73: 3304 14.73 - 29.46: 270 29.46 - 44.19: 55 44.19 - 58.91: 7 58.91 - 73.64: 2 Dihedral angle restraints: 3638 sinusoidal: 1432 harmonic: 2206 Sorted by residual: dihedral pdb=" CB CYS B 41 " pdb=" SG CYS B 41 " pdb=" SG CYS B 115 " pdb=" CB CYS B 115 " ideal model delta sinusoidal sigma weight residual 93.00 166.64 -73.64 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CA TRP A 204 " pdb=" C TRP A 204 " pdb=" N ASN A 205 " pdb=" CA ASN A 205 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASP A 87 " pdb=" CB ASP A 87 " pdb=" CG ASP A 87 " pdb=" OD1 ASP A 87 " ideal model delta sinusoidal sigma weight residual -30.00 -82.66 52.66 1 2.00e+01 2.50e-03 9.44e+00 ... (remaining 3635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 929 0.103 - 0.206: 12 0.206 - 0.309: 0 0.309 - 0.413: 0 0.413 - 0.516: 1 Chirality restraints: 942 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 -1.88 -0.52 2.00e-02 2.50e+03 6.65e+02 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.01e-01 chirality pdb=" CB THR C 107 " pdb=" CA THR C 107 " pdb=" OG1 THR C 107 " pdb=" CG2 THR C 107 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 939 not shown) Planarity restraints: 1048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 338 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 339 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 130 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A 131 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 128 " -0.005 2.00e-02 2.50e+03 1.07e-02 1.15e+00 pdb=" C ASP B 128 " 0.019 2.00e-02 2.50e+03 pdb=" O ASP B 128 " -0.007 2.00e-02 2.50e+03 pdb=" N TYR B 129 " -0.006 2.00e-02 2.50e+03 ... (remaining 1045 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1069 2.76 - 3.30: 5783 3.30 - 3.83: 9983 3.83 - 4.37: 10915 4.37 - 4.90: 19159 Nonbonded interactions: 46909 Sorted by model distance: nonbonded pdb=" OH TYR A 110 " pdb=" O VAL A 394 " model vdw 2.230 2.440 nonbonded pdb=" OG SER B 49 " pdb=" O PRO B 72 " model vdw 2.256 2.440 nonbonded pdb=" O LYS A 201 " pdb=" NE1 TRP B 52 " model vdw 2.296 2.520 nonbonded pdb=" O SER A 477 " pdb=" OG SER A 477 " model vdw 2.303 2.440 nonbonded pdb=" OG SER B 36 " pdb=" O LEU B 102 " model vdw 2.330 2.440 ... (remaining 46904 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 4104 2.51 5 N 962 2.21 5 O 1081 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: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 13.440 Check model and map are aligned: 0.100 Process input model: 20.240 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 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 0.026 6349 Z= 0.118 Angle : 0.596 5.888 8596 Z= 0.305 Chirality : 0.041 0.516 942 Planarity : 0.003 0.033 1047 Dihedral : 10.767 69.682 2229 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.27), residues: 761 helix: -1.23 (0.23), residues: 353 sheet: -2.94 (0.51), residues: 82 loop : -2.92 (0.31), residues: 326 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2148 time to fit residues: 41.5660 Evaluate side-chains 113 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9070 ------------------------------------------------------------------------------- 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: 2.9990 chunk 56 optimal weight: 0.1980 chunk 31 optimal weight: 0.0970 chunk 19 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 194 GLN A 354 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 6349 Z= 0.166 Angle : 0.538 6.887 8596 Z= 0.272 Chirality : 0.039 0.166 942 Planarity : 0.004 0.030 1047 Dihedral : 3.506 21.820 916 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.30), residues: 761 helix: -0.32 (0.27), residues: 350 sheet: -2.38 (0.52), residues: 86 loop : -2.34 (0.35), residues: 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 14 residues processed: 137 average time/residue: 0.1922 time to fit residues: 34.2968 Evaluate side-chains 117 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.622 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0634 time to fit residues: 2.4661 ------------------------------------------------------------------------------- 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: 0.3980 chunk 21 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 chunk 18 optimal weight: 3.9990 chunk 68 optimal weight: 0.0670 chunk 73 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.2274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN C 51 ASN C 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 6349 Z= 0.140 Angle : 0.523 8.450 8596 Z= 0.263 Chirality : 0.039 0.181 942 Planarity : 0.004 0.031 1047 Dihedral : 3.475 20.478 916 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 2.18 % 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: -1.69 (0.31), residues: 761 helix: 0.06 (0.28), residues: 349 sheet: -2.08 (0.51), residues: 97 loop : -2.12 (0.36), residues: 315 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 122 average time/residue: 0.1824 time to fit residues: 29.7721 Evaluate side-chains 111 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.733 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0759 time to fit residues: 1.7134 ------------------------------------------------------------------------------- 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: 2.9990 chunk 51 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2965 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= 0.192 Angle : 0.560 8.700 8596 Z= 0.286 Chirality : 0.040 0.233 942 Planarity : 0.004 0.028 1047 Dihedral : 3.797 21.112 916 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.31), residues: 761 helix: 0.12 (0.28), residues: 353 sheet: -1.92 (0.52), residues: 97 loop : -2.10 (0.36), residues: 311 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 115 average time/residue: 0.1747 time to fit residues: 27.5486 Evaluate side-chains 110 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.713 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0678 time to fit residues: 1.9261 ------------------------------------------------------------------------------- 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: 0.5980 chunk 1 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 6349 Z= 0.218 Angle : 0.588 9.863 8596 Z= 0.296 Chirality : 0.041 0.212 942 Planarity : 0.004 0.049 1047 Dihedral : 4.179 24.153 916 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer Outliers : 2.02 % 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 (0.31), residues: 761 helix: 0.17 (0.28), residues: 352 sheet: -1.69 (0.55), residues: 97 loop : -2.12 (0.35), residues: 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 123 average time/residue: 0.1812 time to fit residues: 29.9398 Evaluate side-chains 118 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0793 time to fit residues: 2.3230 ------------------------------------------------------------------------------- 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: 5.9990 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 72 optimal weight: 0.0270 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 0.0770 chunk 38 optimal weight: 0.0670 chunk 69 optimal weight: 0.1980 overall best weight: 0.2334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 6349 Z= 0.148 Angle : 0.578 9.593 8596 Z= 0.288 Chirality : 0.040 0.218 942 Planarity : 0.003 0.029 1047 Dihedral : 3.977 22.319 916 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 1.40 % 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: -1.37 (0.31), residues: 761 helix: 0.28 (0.28), residues: 353 sheet: -1.48 (0.63), residues: 77 loop : -2.09 (0.35), residues: 331 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 120 average time/residue: 0.1668 time to fit residues: 27.6244 Evaluate side-chains 109 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.677 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0742 time to fit residues: 1.2942 ------------------------------------------------------------------------------- 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: 5.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 28 optimal weight: 0.0370 chunk 43 optimal weight: 0.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3684 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= 0.196 Angle : 0.598 10.213 8596 Z= 0.296 Chirality : 0.040 0.224 942 Planarity : 0.003 0.026 1047 Dihedral : 4.097 22.829 916 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 2.64 % 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: -1.35 (0.31), residues: 761 helix: 0.32 (0.29), residues: 354 sheet: -1.55 (0.62), residues: 77 loop : -2.09 (0.34), residues: 330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 121 average time/residue: 0.1571 time to fit residues: 26.1575 Evaluate side-chains 114 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0802 time to fit residues: 2.4995 ------------------------------------------------------------------------------- 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: 0.7980 chunk 14 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6349 Z= 0.186 Angle : 0.612 10.620 8596 Z= 0.303 Chirality : 0.041 0.237 942 Planarity : 0.004 0.043 1047 Dihedral : 4.125 22.133 916 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer Outliers : 0.93 % 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: -1.27 (0.31), residues: 761 helix: 0.38 (0.29), residues: 352 sheet: -1.49 (0.62), residues: 77 loop : -2.05 (0.34), residues: 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 114 average time/residue: 0.1674 time to fit residues: 26.2787 Evaluate side-chains 112 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 0.718 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0842 time to fit residues: 1.6992 ------------------------------------------------------------------------------- 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: 0.9980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 6349 Z= 0.227 Angle : 0.640 10.708 8596 Z= 0.318 Chirality : 0.041 0.242 942 Planarity : 0.004 0.047 1047 Dihedral : 4.379 23.786 916 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer Outliers : 1.09 % 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: -1.33 (0.31), residues: 761 helix: 0.36 (0.29), residues: 353 sheet: -1.50 (0.57), residues: 86 loop : -2.13 (0.34), residues: 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 114 average time/residue: 0.1843 time to fit residues: 28.2258 Evaluate side-chains 111 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 0.667 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0841 time to fit residues: 1.5819 ------------------------------------------------------------------------------- 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: 0.7980 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6349 Z= 0.199 Angle : 0.649 11.105 8596 Z= 0.320 Chirality : 0.041 0.248 942 Planarity : 0.004 0.046 1047 Dihedral : 4.386 22.577 916 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer Outliers : 0.47 % 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: -1.30 (0.31), residues: 761 helix: 0.45 (0.29), residues: 351 sheet: -1.55 (0.61), residues: 77 loop : -2.15 (0.33), residues: 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 110 average time/residue: 0.1981 time to fit residues: 29.3677 Evaluate side-chains 109 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.743 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0692 time to fit residues: 1.3690 ------------------------------------------------------------------------------- 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: 8.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.0000 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116087 restraints weight = 9655.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119360 restraints weight = 6544.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121618 restraints weight = 5092.216| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4219 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= 0.181 Angle : 0.652 11.146 8596 Z= 0.320 Chirality : 0.041 0.250 942 Planarity : 0.004 0.031 1047 Dihedral : 4.348 23.308 916 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 0.31 % 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: -1.27 (0.31), residues: 761 helix: 0.46 (0.29), residues: 351 sheet: -1.53 (0.60), residues: 77 loop : -2.12 (0.33), residues: 333 =============================================================================== Job complete usr+sys time: 1729.79 seconds wall clock time: 32 minutes 32.08 seconds (1952.08 seconds total)