Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 17:52:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xck_33123/04_2023/7xck_33123.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xck_33123/04_2023/7xck_33123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xck_33123/04_2023/7xck_33123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xck_33123/04_2023/7xck_33123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xck_33123/04_2023/7xck_33123.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xck_33123/04_2023/7xck_33123.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4868 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 3473 2.51 5 N 927 2.21 5 O 1067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 151": "OD1" <-> "OD2" Residue "M PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 5488 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1688 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 210} Chain breaks: 1 Chain: "B" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1615 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "M" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2147 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 16, 'TRANS': 252} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.35, per 1000 atoms: 0.61 Number of scatterers: 5488 At special positions: 0 Unit cell: (113.9, 61.64, 122.61, 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 21 16.00 O 1067 8.00 N 927 7.00 C 3473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 210 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 336 " - pdb=" SG CYS M 361 " distance=2.03 Simple disulfide: pdb=" SG CYS M 379 " - pdb=" SG CYS M 432 " distance=2.04 Simple disulfide: pdb=" SG CYS M 480 " - pdb=" SG CYS M 488 " distance=2.03 Simple disulfide: pdb=" SG CYS M 538 " - pdb=" SG CYS M 590 " 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=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN M 343 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 790.1 milliseconds 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1302 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 14 sheets defined 9.7% alpha, 38.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.646A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.942A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 80 through 84 removed outlier: 4.031A pdb=" N PHE B 84 " --> pdb=" O PRO B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 removed outlier: 3.542A pdb=" N LYS B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 343 Processing helix chain 'M' and resid 365 through 369 Processing helix chain 'M' and resid 383 through 390 removed outlier: 3.529A pdb=" N LEU M 387 " --> pdb=" O PRO M 384 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN M 388 " --> pdb=" O THR M 385 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU M 390 " --> pdb=" O LEU M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 403 through 410 removed outlier: 3.521A pdb=" N GLU M 406 " --> pdb=" O ARG M 403 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL M 407 " --> pdb=" O GLY M 404 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG M 408 " --> pdb=" O ASP M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 422 Processing helix chain 'M' and resid 438 through 443 removed outlier: 3.707A pdb=" N SER M 443 " --> pdb=" O ASN M 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.515A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN A 116 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.515A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.127A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.127A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.402A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.402A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.957A pdb=" N VAL B 133 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 138 " --> pdb=" O TYR B 173 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 145 through 149 Processing sheet with id=AB3, first strand: chain 'M' and resid 325 through 328 removed outlier: 5.842A pdb=" N ASP M 574 " --> pdb=" O ILE M 587 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY M 566 " --> pdb=" O ASP M 574 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 354 through 358 Processing sheet with id=AB5, first strand: chain 'M' and resid 452 through 454 209 hydrogen bonds defined for protein. 513 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 948 1.32 - 1.45: 1605 1.45 - 1.58: 3044 1.58 - 1.71: 0 1.71 - 1.84: 24 Bond restraints: 5621 Sorted by residual: bond pdb=" C ALA M 344 " pdb=" N THR M 345 " ideal model delta sigma weight residual 1.335 1.278 0.057 1.25e-02 6.40e+03 2.05e+01 bond pdb=" CA ALA M 344 " pdb=" CB ALA M 344 " ideal model delta sigma weight residual 1.528 1.474 0.054 1.58e-02 4.01e+03 1.15e+01 bond pdb=" C ALA M 344 " pdb=" O ALA M 344 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.20e-02 6.94e+03 8.18e+00 bond pdb=" C ASN M 343 " pdb=" O ASN M 343 " ideal model delta sigma weight residual 1.235 1.197 0.038 1.32e-02 5.74e+03 8.17e+00 bond pdb=" CA ALA M 344 " pdb=" C ALA M 344 " ideal model delta sigma weight residual 1.524 1.486 0.038 1.33e-02 5.65e+03 8.00e+00 ... (remaining 5616 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.75: 187 106.75 - 113.56: 3016 113.56 - 120.37: 1949 120.37 - 127.18: 2434 127.18 - 133.99: 58 Bond angle restraints: 7644 Sorted by residual: angle pdb=" CA ASN M 334 " pdb=" C ASN M 334 " pdb=" O ASN M 334 " ideal model delta sigma weight residual 121.15 116.26 4.89 1.10e+00 8.26e-01 1.98e+01 angle pdb=" C VAL B 150 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " ideal model delta sigma weight residual 121.54 129.19 -7.65 1.91e+00 2.74e-01 1.60e+01 angle pdb=" C ASN M 343 " pdb=" CA ASN M 343 " pdb=" CB ASN M 343 " ideal model delta sigma weight residual 111.02 104.60 6.42 1.61e+00 3.86e-01 1.59e+01 angle pdb=" C PRO A 161 " pdb=" N GLU A 162 " pdb=" CA GLU A 162 " ideal model delta sigma weight residual 120.26 125.14 -4.88 1.34e+00 5.57e-01 1.33e+01 angle pdb=" C SER B 95 " pdb=" CA SER B 95 " pdb=" CB SER B 95 " ideal model delta sigma weight residual 115.89 111.20 4.69 1.32e+00 5.74e-01 1.26e+01 ... (remaining 7639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 3057 17.59 - 35.17: 220 35.17 - 52.76: 47 52.76 - 70.34: 5 70.34 - 87.93: 4 Dihedral angle restraints: 3333 sinusoidal: 1297 harmonic: 2036 Sorted by residual: dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 210 " pdb=" CB CYS A 210 " ideal model delta sinusoidal sigma weight residual 93.00 162.64 -69.64 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS M 538 " pdb=" SG CYS M 538 " pdb=" SG CYS M 590 " pdb=" CB CYS M 590 " ideal model delta sinusoidal sigma weight residual -86.00 -38.35 -47.65 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS M 379 " pdb=" SG CYS M 379 " pdb=" SG CYS M 432 " pdb=" CB CYS M 432 " ideal model delta sinusoidal sigma weight residual -86.00 -51.56 -34.44 1 1.00e+01 1.00e-02 1.68e+01 ... (remaining 3330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 855 0.142 - 0.284: 2 0.284 - 0.425: 0 0.425 - 0.567: 0 0.567 - 0.709: 1 Chirality restraints: 858 Sorted by residual: chirality pdb=" C1 FUC C 3 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 3 " pdb=" O5 FUC C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.19e+01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN M 343 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA VAL A 37 " pdb=" N VAL A 37 " pdb=" C VAL A 37 " pdb=" CB VAL A 37 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 855 not shown) Planarity restraints: 982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.045 2.00e-02 2.50e+03 3.72e-02 1.73e+01 pdb=" C7 NAG C 1 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.060 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.041 2.00e-02 2.50e+03 3.36e-02 1.41e+01 pdb=" C7 NAG C 2 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.052 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA M 520 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO M 521 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO M 521 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO M 521 " 0.036 5.00e-02 4.00e+02 ... (remaining 979 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 246 2.72 - 3.27: 5007 3.27 - 3.81: 8362 3.81 - 4.36: 10652 4.36 - 4.90: 18600 Nonbonded interactions: 42867 Sorted by model distance: nonbonded pdb=" OH TYR M 369 " pdb=" O PRO M 384 " model vdw 2.179 2.440 nonbonded pdb=" OG SER B 64 " pdb=" OG1 THR B 75 " model vdw 2.198 2.440 nonbonded pdb=" OG1 THR A 149 " pdb=" O VAL A 198 " model vdw 2.228 2.440 nonbonded pdb=" OE1 GLU B 105 " pdb=" OH TYR B 173 " model vdw 2.296 2.440 nonbonded pdb=" O ASP M 442 " pdb=" ND2 ASN M 448 " model vdw 2.307 2.520 ... (remaining 42862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 27.930 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.840 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 5621 Z= 0.251 Angle : 0.713 11.067 7644 Z= 0.389 Chirality : 0.052 0.709 858 Planarity : 0.006 0.065 981 Dihedral : 12.659 87.930 2007 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.60 % Favored : 95.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.32), residues: 696 helix: -3.99 (0.85), residues: 20 sheet: 0.21 (0.33), residues: 271 loop : -0.98 (0.31), residues: 405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.675 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 1.4646 time to fit residues: 105.1935 Evaluate side-chains 57 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.604 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 417 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 5621 Z= 0.388 Angle : 0.696 8.926 7644 Z= 0.362 Chirality : 0.050 0.168 858 Planarity : 0.006 0.069 981 Dihedral : 5.322 20.401 764 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.90 % Favored : 92.96 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.15 (0.33), residues: 696 helix: -4.53 (0.46), residues: 26 sheet: 0.01 (0.32), residues: 286 loop : -1.07 (0.32), residues: 384 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.709 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 73 average time/residue: 1.4403 time to fit residues: 109.3987 Evaluate side-chains 66 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.685 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0923 time to fit residues: 1.0376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 5621 Z= 0.317 Angle : 0.653 10.084 7644 Z= 0.339 Chirality : 0.048 0.161 858 Planarity : 0.006 0.069 981 Dihedral : 5.232 19.696 764 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.32 % Favored : 93.53 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.07 (0.32), residues: 696 helix: -4.53 (0.44), residues: 26 sheet: 0.14 (0.32), residues: 280 loop : -1.07 (0.32), residues: 390 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 0.690 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 71 average time/residue: 1.3792 time to fit residues: 102.3068 Evaluate side-chains 69 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.653 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.4131 time to fit residues: 3.2126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 5621 Z= 0.449 Angle : 0.722 10.040 7644 Z= 0.376 Chirality : 0.051 0.182 858 Planarity : 0.007 0.073 981 Dihedral : 5.608 21.497 764 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer Outliers : 4.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.29 (0.32), residues: 696 helix: -4.64 (0.41), residues: 24 sheet: -0.05 (0.31), residues: 289 loop : -1.24 (0.32), residues: 383 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 55 time to evaluate : 0.670 Fit side-chains outliers start: 29 outliers final: 12 residues processed: 76 average time/residue: 1.1380 time to fit residues: 90.9730 Evaluate side-chains 65 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.672 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.8809 time to fit residues: 2.7645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.0170 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.023 5621 Z= 0.230 Angle : 0.621 10.186 7644 Z= 0.319 Chirality : 0.046 0.152 858 Planarity : 0.006 0.073 981 Dihedral : 5.113 18.039 764 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 4.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.06 (0.32), residues: 696 helix: -4.55 (0.45), residues: 26 sheet: 0.14 (0.32), residues: 283 loop : -1.06 (0.32), residues: 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 53 time to evaluate : 0.693 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 72 average time/residue: 1.2552 time to fit residues: 94.7730 Evaluate side-chains 67 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.0717 time to fit residues: 1.3182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5621 Z= 0.207 Angle : 0.602 9.856 7644 Z= 0.308 Chirality : 0.045 0.147 858 Planarity : 0.005 0.069 981 Dihedral : 4.917 18.023 764 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.91 (0.33), residues: 696 helix: -4.47 (0.49), residues: 26 sheet: 0.26 (0.32), residues: 283 loop : -0.98 (0.33), residues: 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 0.706 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 69 average time/residue: 1.2047 time to fit residues: 87.2905 Evaluate side-chains 67 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.588 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.0463 time to fit residues: 1.0603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.7980 chunk 37 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 41 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 5621 Z= 0.311 Angle : 0.671 10.921 7644 Z= 0.345 Chirality : 0.049 0.322 858 Planarity : 0.006 0.071 981 Dihedral : 5.156 17.919 764 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 4.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.97 (0.33), residues: 696 helix: -4.45 (0.53), residues: 24 sheet: 0.26 (0.32), residues: 283 loop : -1.09 (0.32), residues: 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 51 time to evaluate : 0.610 Fit side-chains outliers start: 29 outliers final: 17 residues processed: 74 average time/residue: 1.1562 time to fit residues: 89.9335 Evaluate side-chains 69 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 0.659 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.0532 time to fit residues: 1.1840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 5621 Z= 0.329 Angle : 0.712 14.023 7644 Z= 0.362 Chirality : 0.049 0.346 858 Planarity : 0.006 0.072 981 Dihedral : 5.306 22.340 764 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.99 (0.33), residues: 696 helix: -4.46 (0.53), residues: 24 sheet: 0.29 (0.32), residues: 283 loop : -1.14 (0.32), residues: 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 54 time to evaluate : 0.668 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 70 average time/residue: 1.2984 time to fit residues: 95.1193 Evaluate side-chains 69 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 53 time to evaluate : 0.660 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.0967 time to fit residues: 1.2167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.5980 chunk 48 optimal weight: 0.1980 chunk 19 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 5621 Z= 0.166 Angle : 0.616 11.968 7644 Z= 0.310 Chirality : 0.045 0.268 858 Planarity : 0.005 0.068 981 Dihedral : 4.743 21.049 764 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.33), residues: 696 helix: -4.39 (0.57), residues: 26 sheet: 0.63 (0.34), residues: 264 loop : -1.03 (0.31), residues: 406 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 0.707 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 69 average time/residue: 1.3242 time to fit residues: 95.7588 Evaluate side-chains 66 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 0.9553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 5621 Z= 0.383 Angle : 0.729 13.537 7644 Z= 0.371 Chirality : 0.050 0.313 858 Planarity : 0.006 0.070 981 Dihedral : 5.328 23.810 764 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.87 (0.33), residues: 696 helix: -4.37 (0.57), residues: 24 sheet: 0.41 (0.32), residues: 279 loop : -1.08 (0.32), residues: 393 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.640 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 13 residues processed: 66 average time/residue: 1.2255 time to fit residues: 84.7440 Evaluate side-chains 67 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.636 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 0.8568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.184127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.121588 restraints weight = 6093.055| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.42 r_work: 0.3349 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 5621 Z= 0.213 Angle : 0.653 13.283 7644 Z= 0.329 Chirality : 0.046 0.279 858 Planarity : 0.005 0.069 981 Dihedral : 5.001 22.027 764 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.82 (0.33), residues: 696 helix: -4.37 (0.57), residues: 26 sheet: 0.37 (0.32), residues: 282 loop : -0.97 (0.32), residues: 388 =============================================================================== Job complete usr+sys time: 2782.68 seconds wall clock time: 50 minutes 7.59 seconds (3007.59 seconds total)