Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 14:54:47 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/12_2021/7m3n_23658.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/12_2021/7m3n_23658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/12_2021/7m3n_23658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/12_2021/7m3n_23658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/12_2021/7m3n_23658.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/12_2021/7m3n_23658.pdb" } resolution = 2.4 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= 0.005 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 6004 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 842 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 103, 'PCIS': 1} Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 924 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "A" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 38, 'TRANS': 492, 'PCIS': 1} Chain breaks: 2 Time building chain proxies: 3.75, per 1000 atoms: 0.62 Number of scatterers: 6004 At special positions: 0 Unit cell: (82.5, 113.3, 105.6, 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 1144 8.00 N 1024 7.00 C 3813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 494 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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: 2.16 Conformation dependent library (CDL) restraints added in 966.0 milliseconds 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 17 sheets defined 9.6% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.611A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.533A pdb=" N VAL A 119 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.979A pdb=" N MET A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.853A pdb=" N VAL A 241 " --> pdb=" O PRO A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.037A pdb=" N LEU A 285 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 removed outlier: 4.099A pdb=" N ARG A 313 " --> pdb=" O GLN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.192A pdb=" N GLY A 385 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 removed outlier: 3.556A pdb=" N ASP A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.722A pdb=" N PHE A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.692A pdb=" N ASN A 560 " --> pdb=" O ASN A 557 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 561 " --> pdb=" O GLN A 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 557 through 561' Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.687A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.148A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.685A pdb=" N VAL L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.526A pdb=" N SER L 65 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.443A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.979A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 60 removed outlier: 6.655A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 60 removed outlier: 6.655A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 49 through 53 removed outlier: 6.761A pdb=" N TYR A 524 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL A 149 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP A 526 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN A 147 " --> pdb=" O ASP A 526 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP A 528 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A 145 " --> pdb=" O TRP A 528 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS A 530 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN A 143 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS A 532 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE A 141 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A 534 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 538 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A 135 " --> pdb=" O LYS A 538 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLN A 143 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLY A 264 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE A 145 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ALA A 262 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 164 through 167 Processing sheet with id=AA9, first strand: chain 'A' and resid 80 through 84 removed outlier: 4.235A pdb=" N ALA A 103 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TRP A 208 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TRP A 109 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR A 206 " --> pdb=" O TRP A 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 80 through 84 removed outlier: 5.963A pdb=" N VAL A 502 " --> pdb=" O PRO A 108 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 497 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 215 through 218 removed outlier: 6.336A pdb=" N ASP A 215 " --> pdb=" O HIS A 234 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 276 through 278 Processing sheet with id=AB4, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.357A pdb=" N GLU A 335 " --> pdb=" O ALA A 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 345 through 348 Processing sheet with id=AB6, first strand: chain 'A' and resid 377 through 380 Processing sheet with id=AB7, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AB8, first strand: chain 'A' and resid 470 through 472 removed outlier: 6.555A pdb=" N ASP A 471 " --> pdb=" O CYS A 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 167 hydrogen bonds defined for protein. 387 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: 1.98 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1949 1.34 - 1.46: 1564 1.46 - 1.58: 2622 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 6173 Sorted by residual: bond pdb=" CA ILE A 219 " pdb=" CB ILE A 219 " ideal model delta sigma weight residual 1.537 1.522 0.015 1.29e-02 6.01e+03 1.36e+00 bond pdb=" CG1 ILE A 101 " pdb=" CD1 ILE A 101 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.09e+00 bond pdb=" CA ASP A 269 " pdb=" C ASP A 269 " ideal model delta sigma weight residual 1.530 1.519 0.011 1.08e-02 8.57e+03 1.04e+00 bond pdb=" CB THR A 230 " pdb=" CG2 THR A 230 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.49e-01 bond pdb=" CB GLN A 143 " pdb=" CG GLN A 143 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 7.83e-01 ... (remaining 6168 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.56: 222 106.56 - 113.43: 3265 113.43 - 120.31: 2160 120.31 - 127.18: 2674 127.18 - 134.06: 99 Bond angle restraints: 8420 Sorted by residual: angle pdb=" C GLY H 54 " pdb=" N ASP H 55 " pdb=" CA ASP H 55 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.48e+00 angle pdb=" N ALA L 32 " pdb=" CA ALA L 32 " pdb=" C ALA L 32 " ideal model delta sigma weight residual 111.30 114.69 -3.39 1.36e+00 5.41e-01 6.21e+00 angle pdb=" N PRO A 423 " pdb=" CA PRO A 423 " pdb=" C PRO A 423 " ideal model delta sigma weight residual 112.47 107.54 4.93 2.06e+00 2.36e-01 5.73e+00 angle pdb=" C LYS H 74 " pdb=" N SER H 75 " pdb=" CA SER H 75 " ideal model delta sigma weight residual 121.54 125.91 -4.37 1.91e+00 2.74e-01 5.23e+00 angle pdb=" CA ASN H 83 " pdb=" C ASN H 83 " pdb=" N ARG H 84 " ideal model delta sigma weight residual 114.17 117.47 -3.30 1.45e+00 4.76e-01 5.18e+00 ... (remaining 8415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 3131 16.94 - 33.88: 353 33.88 - 50.82: 86 50.82 - 67.76: 30 67.76 - 84.70: 6 Dihedral angle restraints: 3606 sinusoidal: 1417 harmonic: 2189 Sorted by residual: dihedral pdb=" CB CYS A 490 " pdb=" SG CYS A 490 " pdb=" SG CYS A 494 " pdb=" CB CYS A 494 " ideal model delta sinusoidal sigma weight residual 93.00 37.65 55.35 1 1.00e+01 1.00e-02 4.14e+01 dihedral pdb=" CA THR L 31 " pdb=" C THR L 31 " pdb=" N ALA L 32 " pdb=" CA ALA L 32 " ideal model delta harmonic sigma weight residual 180.00 151.43 28.57 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASN A 421 " pdb=" C ASN A 421 " pdb=" N LEU A 422 " pdb=" CA LEU A 422 " ideal model delta harmonic sigma weight residual -180.00 -156.12 -23.88 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 3603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 483 0.028 - 0.057: 256 0.057 - 0.085: 99 0.085 - 0.113: 52 0.113 - 0.141: 17 Chirality restraints: 907 Sorted by residual: chirality pdb=" CA ILE L 39 " pdb=" N ILE L 39 " pdb=" C ILE L 39 " pdb=" CB ILE L 39 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE A 357 " pdb=" N ILE A 357 " pdb=" C ILE A 357 " pdb=" CB ILE A 357 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE A 306 " pdb=" N ILE A 306 " pdb=" C ILE A 306 " pdb=" CB ILE A 306 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 904 not shown) Planarity restraints: 1096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 122 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.85e+00 pdb=" N PRO A 123 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 464 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO A 465 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 465 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 465 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 55 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C ASP H 55 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP H 55 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY H 56 " 0.010 2.00e-02 2.50e+03 ... (remaining 1093 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 259 2.71 - 3.26: 5360 3.26 - 3.81: 9281 3.81 - 4.35: 11759 4.35 - 4.90: 20009 Nonbonded interactions: 46668 Sorted by model distance: nonbonded pdb=" OG SER L 43 " pdb=" O GLY H 110 " model vdw 2.168 2.440 nonbonded pdb=" NH2 ARG A 382 " pdb=" O GLY A 392 " model vdw 2.220 2.520 nonbonded pdb=" OG SER A 65 " pdb=" O VAL A 119 " model vdw 2.287 2.440 nonbonded pdb=" O THR A 301 " pdb=" OG1 THR A 301 " model vdw 2.324 2.440 nonbonded pdb=" ND2 ASN A 443 " pdb=" OG1 THR A 445 " model vdw 2.346 2.520 ... (remaining 46663 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 23 5.16 5 C 3813 2.51 5 N 1024 2.21 5 O 1144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Write .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: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 19.170 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.060 Process input model: 21.200 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.370 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 57.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 0.005 0.044 6173 Z= 0.303 Angle : 0.630 8.042 8420 Z= 0.358 Chirality : 0.044 0.141 907 Planarity : 0.005 0.060 1096 Dihedral : 15.949 84.702 2197 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.27 % Favored : 95.59 % Rotamer Outliers : 4.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.53 (0.26), residues: 749 helix: -2.08 (1.08), residues: 10 sheet: -1.02 (0.30), residues: 248 loop : -2.14 (0.22), residues: 491 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 0.748 Fit side-chains outliers start: 28 outliers final: 13 residues processed: 175 average time/residue: 0.8545 time to fit residues: 158.7967 Evaluate side-chains 163 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 0.704 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.5149 time to fit residues: 3.1929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.0770 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN L 42 GLN L 53 ASN L 89 GLN H 39 GLN H 43 GLN H 81 GLN A 72 ASN A 93 ASN A 104 GLN A 137 HIS A 143 GLN A 222 HIS A 242 GLN A 280 GLN A 296 GLN A 302 ASN A 309 GLN A 404 GLN A 417 ASN A 428 ASN A 443 ASN A 446 ASN A 459 ASN A 468 GLN A 560 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 6173 Z= 0.189 Angle : 0.525 8.095 8420 Z= 0.271 Chirality : 0.043 0.145 907 Planarity : 0.004 0.065 1096 Dihedral : 4.830 26.861 821 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.01 % Favored : 95.86 % Rotamer Outliers : 5.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.76 (0.27), residues: 749 helix: -2.04 (0.87), residues: 16 sheet: -0.40 (0.31), residues: 243 loop : -1.62 (0.24), residues: 490 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 0.677 Fit side-chains outliers start: 34 outliers final: 17 residues processed: 174 average time/residue: 0.8534 time to fit residues: 157.7566 Evaluate side-chains 166 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 0.678 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 6 average time/residue: 0.5911 time to fit residues: 4.7565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 chunk 18 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 72 optimal weight: 0.1980 chunk 59 optimal weight: 0.0670 chunk 66 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN A 137 HIS A 384 HIS A 404 GLN A 458 ASN A 459 ASN A 466 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 6173 Z= 0.137 Angle : 0.482 6.957 8420 Z= 0.246 Chirality : 0.042 0.158 907 Planarity : 0.004 0.067 1096 Dihedral : 4.371 22.941 821 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 4.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.21 (0.28), residues: 749 helix: -1.42 (0.99), residues: 16 sheet: -0.15 (0.32), residues: 255 loop : -1.19 (0.26), residues: 478 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 0.615 Fit side-chains outliers start: 32 outliers final: 17 residues processed: 174 average time/residue: 0.8282 time to fit residues: 153.2653 Evaluate side-chains 167 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 6 average time/residue: 0.5962 time to fit residues: 4.8195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 64 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 8 HIS L 89 GLN A 137 HIS A 167 ASN A 404 GLN A 459 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 6173 Z= 0.173 Angle : 0.502 7.136 8420 Z= 0.255 Chirality : 0.043 0.155 907 Planarity : 0.004 0.068 1096 Dihedral : 4.416 22.954 821 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 3.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.03 (0.28), residues: 749 helix: -1.45 (0.97), residues: 16 sheet: -0.00 (0.32), residues: 255 loop : -1.07 (0.26), residues: 478 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 0.716 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 166 average time/residue: 0.8902 time to fit residues: 156.9589 Evaluate side-chains 164 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 0.4102 time to fit residues: 3.2681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN A 137 HIS A 167 ASN A 404 GLN A 459 ASN A 483 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.093 6173 Z= 0.629 Angle : 0.666 8.625 8420 Z= 0.344 Chirality : 0.050 0.168 907 Planarity : 0.005 0.076 1096 Dihedral : 5.470 30.509 821 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.34 % Favored : 94.53 % Rotamer Outliers : 5.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.17 (0.28), residues: 749 helix: -1.43 (0.97), residues: 16 sheet: 0.22 (0.33), residues: 237 loop : -1.33 (0.25), residues: 496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 154 time to evaluate : 0.719 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 29 residues processed: 171 average time/residue: 0.8954 time to fit residues: 162.6101 Evaluate side-chains 182 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 0.716 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 15 residues processed: 14 average time/residue: 0.2955 time to fit residues: 5.7370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN H 81 GLN A 137 HIS A 404 GLN A 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 6173 Z= 0.185 Angle : 0.510 7.389 8420 Z= 0.261 Chirality : 0.043 0.147 907 Planarity : 0.004 0.069 1096 Dihedral : 4.742 25.283 821 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.87 % Favored : 95.99 % Rotamer Outliers : 4.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.29), residues: 749 helix: -1.44 (0.92), residues: 16 sheet: 0.28 (0.33), residues: 239 loop : -1.05 (0.25), residues: 494 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 0.734 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 21 residues processed: 167 average time/residue: 0.9031 time to fit residues: 159.8592 Evaluate side-chains 159 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 0.694 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 16 residues processed: 5 average time/residue: 0.3844 time to fit residues: 3.1016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.0370 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 32 optimal weight: 0.0670 chunk 28 optimal weight: 0.8980 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN A 137 HIS A 404 GLN A 459 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 6173 Z= 0.167 Angle : 0.500 7.054 8420 Z= 0.255 Chirality : 0.043 0.146 907 Planarity : 0.004 0.067 1096 Dihedral : 4.469 24.010 821 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 4.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.29), residues: 749 helix: -1.30 (0.96), residues: 16 sheet: 0.16 (0.32), residues: 255 loop : -0.85 (0.27), residues: 478 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 0.878 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 20 residues processed: 155 average time/residue: 0.9865 time to fit residues: 162.1030 Evaluate side-chains 151 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 0.710 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 5 average time/residue: 0.7416 time to fit residues: 4.9367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.0470 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN A 137 HIS A 404 GLN A 459 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 6173 Z= 0.187 Angle : 0.506 6.873 8420 Z= 0.259 Chirality : 0.043 0.146 907 Planarity : 0.004 0.065 1096 Dihedral : 4.487 24.008 821 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.01 % Favored : 95.86 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.29), residues: 749 helix: -0.98 (1.07), residues: 16 sheet: 0.48 (0.33), residues: 239 loop : -0.86 (0.26), residues: 494 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 0.712 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 20 residues processed: 159 average time/residue: 0.9448 time to fit residues: 158.9694 Evaluate side-chains 157 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.4626 time to fit residues: 3.0016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN A 137 HIS A 404 GLN A 459 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 6173 Z= 0.158 Angle : 0.523 10.365 8420 Z= 0.264 Chirality : 0.043 0.146 907 Planarity : 0.004 0.064 1096 Dihedral : 4.400 22.904 821 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.29), residues: 749 helix: -0.12 (1.36), residues: 10 sheet: 0.37 (0.33), residues: 255 loop : -0.70 (0.27), residues: 484 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 0.648 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 19 residues processed: 156 average time/residue: 0.9560 time to fit residues: 158.0852 Evaluate side-chains 155 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.9035 time to fit residues: 2.9255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 8.9990 chunk 48 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 45 optimal weight: 0.0670 chunk 35 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.6924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN A 137 HIS A 404 GLN A 459 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 6173 Z= 0.282 Angle : 0.560 7.574 8420 Z= 0.287 Chirality : 0.044 0.146 907 Planarity : 0.004 0.066 1096 Dihedral : 4.769 26.115 821 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.41 % Favored : 95.46 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.29), residues: 749 helix: -0.83 (1.12), residues: 16 sheet: 0.43 (0.33), residues: 243 loop : -0.83 (0.26), residues: 490 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 0.722 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 19 residues processed: 152 average time/residue: 0.9702 time to fit residues: 155.7662 Evaluate side-chains 151 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 0.704 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.0548 time to fit residues: 1.2529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN A 137 HIS A 302 ASN A 404 GLN A 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.123281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109128 restraints weight = 8292.711| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.80 r_work: 0.3429 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 1.59 restraints_weight: 0.2500 r_work: 0.3400 rms_B_bonded: 1.66 restraints_weight: 0.1250 r_work: 0.3384 rms_B_bonded: 1.79 restraints_weight: 0.0625 r_work: 0.3366 rms_B_bonded: 1.97 restraints_weight: 0.0312 r_work: 0.3345 rms_B_bonded: 2.22 restraints_weight: 0.0156 r_work: 0.3322 rms_B_bonded: 2.53 restraints_weight: 0.0078 r_work: 0.3295 rms_B_bonded: 2.91 restraints_weight: 0.0039 r_work: 0.3264 rms_B_bonded: 3.38 restraints_weight: 0.0020 r_work: 0.3228 rms_B_bonded: 3.95 restraints_weight: 0.0010 r_work: 0.3186 rms_B_bonded: 4.65 restraints_weight: 0.0005 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 6173 Z= 0.326 Angle : 0.577 6.962 8420 Z= 0.296 Chirality : 0.045 0.146 907 Planarity : 0.004 0.067 1096 Dihedral : 4.922 27.352 821 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.54 % Favored : 95.33 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.29), residues: 749 helix: -1.32 (0.98), residues: 16 sheet: 0.39 (0.33), residues: 243 loop : -0.84 (0.26), residues: 490 =============================================================================== Job complete usr+sys time: 3013.60 seconds wall clock time: 53 minutes 55.49 seconds (3235.49 seconds total)