Starting phenix.real_space_refine (version: dev) on Thu May 12 16:14:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0c_24103/05_2022/7n0c_24103.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0c_24103/05_2022/7n0c_24103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0c_24103/05_2022/7n0c_24103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0c_24103/05_2022/7n0c_24103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0c_24103/05_2022/7n0c_24103.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0c_24103/05_2022/7n0c_24103.pdb" } resolution = 3.4 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= 0.002 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 6088 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "B" Number of atoms: 4090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4090 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 26, 'TRANS': 486} Chain breaks: 1 Chain: "T" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 529 Classifications: {'RNA': 25} Modifications used: {'rna3p_pyr': 12, 'rna3p_pur': 12, 'rna2p_pyr': 1} Link IDs: {'rna3p': 23, 'rna2p': 1} Chain: "D" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 506 Classifications: {'RNA': 24} Modifications used: {'rna3p_pyr': 12, 'rna3p_pur': 12} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' ZN': 3, ' MG': 2} Classifications: {'undetermined': 5, 'water': 1} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 520 SG CYS A 74 40.023 24.791 92.919 1.00 51.61 S ATOM 546 SG CYS A 77 36.858 25.756 93.856 1.00 51.71 S ATOM 651 SG CYS A 90 37.756 22.498 94.187 1.00 57.18 S ATOM 854 SG CYS A 117 52.155 10.429 99.974 1.00112.87 S ATOM 874 SG CYS A 120 52.595 10.897 103.370 1.00118.76 S ATOM 935 SG CYS A 128 55.207 11.780 101.062 1.00109.13 S ATOM 947 SG CYS A 130 55.533 8.590 102.165 1.00128.22 S ATOM 2582 SG CYS B 207 44.467 25.564 61.321 1.00 62.28 S ATOM 2602 SG CYS B 210 45.850 26.017 57.879 1.00 73.07 S ATOM 2723 SG CYS B 226 43.066 27.801 59.072 1.00 56.89 S ATOM 3023 SG CYS B 261 24.861 55.828 57.812 1.00 65.13 S ATOM 3153 SG CYS B 279 27.911 54.398 59.550 1.00 44.17 S ATOM 4543 SG CYS B 452 49.557 45.528 11.477 1.00134.04 S ATOM 4657 SG CYS B 477 45.734 45.992 12.975 1.00138.24 S ATOM 4699 SG CYS B 484 48.139 43.581 13.594 1.00139.40 S Time building chain proxies: 4.31, per 1000 atoms: 0.71 Number of scatterers: 6088 At special positions: 0 Unit cell: (70.488, 89.712, 144.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 52 16.00 P 49 15.00 Mg 2 11.99 O 1262 8.00 N 1033 7.00 C 3685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 947.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 77 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 90 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 74 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 130 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 120 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 117 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 229 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 226 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 210 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 207 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 264 " pdb="ZN ZN B 604 " - pdb=" NE2 HIS B 257 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 279 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 261 " pdb=" ZN B 605 " pdb="ZN ZN B 605 " - pdb=" ND1 HIS B 487 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 484 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 477 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 452 " Number of angles added : 17 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1204 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 26.6% alpha, 12.1% beta 23 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 85 through 89 removed outlier: 4.249A pdb=" N PHE A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.067A pdb=" N LYS A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.595A pdb=" N VAL B 29 " --> pdb=" O HIS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 187 through 194 removed outlier: 3.844A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.850A pdb=" N GLY B 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 253 through 258 removed outlier: 3.654A pdb=" N ASP B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 275 through 287 removed outlier: 3.841A pdb=" N CYS B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 325 removed outlier: 3.584A pdb=" N ASN B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 318 " --> pdb=" O HIS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.931A pdb=" N VAL B 437 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.589A pdb=" N GLY B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 505 removed outlier: 4.313A pdb=" N ASN B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU B 490 " --> pdb=" O HIS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 523 removed outlier: 3.754A pdb=" N ASN B 521 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55 removed outlier: 4.365A pdb=" N TYR B 124 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 116 through 118 removed outlier: 5.519A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 223 through 225 removed outlier: 3.726A pdb=" N THR B 223 " --> pdb=" O SER B 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 364 through 365 removed outlier: 7.020A pdb=" N LEU B 329 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N TYR B 351 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ASP B 331 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 381 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 397 through 401 Processing sheet with id=AA7, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'B' and resid 446 through 447 removed outlier: 5.938A pdb=" N TYR B 446 " --> pdb=" O ILE B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 125 hydrogen bonds defined for protein. 324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 860 1.29 - 1.42: 2016 1.42 - 1.56: 3298 1.56 - 1.69: 97 1.69 - 1.83: 68 Bond restraints: 6339 Sorted by residual: bond pdb=" C PRO B 106 " pdb=" O PRO B 106 " ideal model delta sigma weight residual 1.233 1.151 0.082 1.06e-02 8.90e+03 6.06e+01 bond pdb=" CA PRO B 106 " pdb=" CB PRO B 106 " ideal model delta sigma weight residual 1.533 1.485 0.048 1.26e-02 6.30e+03 1.44e+01 bond pdb=" N LEU B 105 " pdb=" CA LEU B 105 " ideal model delta sigma weight residual 1.452 1.499 -0.047 1.41e-02 5.03e+03 1.12e+01 bond pdb=" C ASN B 104 " pdb=" O ASN B 104 " ideal model delta sigma weight residual 1.234 1.195 0.039 1.19e-02 7.06e+03 1.06e+01 bond pdb=" C LEU B 105 " pdb=" N PRO B 106 " ideal model delta sigma weight residual 1.334 1.368 -0.034 1.11e-02 8.12e+03 9.49e+00 ... (remaining 6334 not shown) Histogram of bond angle deviations from ideal: 97.69 - 105.00: 329 105.00 - 112.31: 3228 112.31 - 119.62: 2109 119.62 - 126.93: 2979 126.93 - 134.24: 196 Bond angle restraints: 8841 Sorted by residual: angle pdb=" CA PRO B 106 " pdb=" C PRO B 106 " pdb=" O PRO B 106 " ideal model delta sigma weight residual 120.97 111.88 9.09 1.17e+00 7.31e-01 6.03e+01 angle pdb=" C PRO B 106 " pdb=" CA PRO B 106 " pdb=" CB PRO B 106 " ideal model delta sigma weight residual 111.11 103.39 7.72 1.17e+00 7.31e-01 4.35e+01 angle pdb=" CA PRO B 106 " pdb=" C PRO B 106 " pdb=" N LEU B 107 " ideal model delta sigma weight residual 115.93 123.67 -7.74 1.26e+00 6.30e-01 3.78e+01 angle pdb=" CA LEU B 105 " pdb=" C LEU B 105 " pdb=" N PRO B 106 " ideal model delta sigma weight residual 117.67 123.60 -5.93 1.01e+00 9.80e-01 3.45e+01 angle pdb=" N VAL B 167 " pdb=" CA VAL B 167 " pdb=" C VAL B 167 " ideal model delta sigma weight residual 112.90 107.43 5.47 9.60e-01 1.09e+00 3.24e+01 ... (remaining 8836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.34: 3557 34.34 - 68.68: 62 68.68 - 103.02: 4 103.02 - 137.36: 0 137.36 - 171.70: 1 Dihedral angle restraints: 3624 sinusoidal: 1749 harmonic: 1875 Sorted by residual: dihedral pdb=" O4' U T 6 " pdb=" C1' U T 6 " pdb=" N1 U T 6 " pdb=" C2 U T 6 " ideal model delta sinusoidal sigma weight residual 232.00 60.30 171.70 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" CA HIS B 268 " pdb=" C HIS B 268 " pdb=" N VAL B 269 " pdb=" CA VAL B 269 " ideal model delta harmonic sigma weight residual 180.00 156.65 23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA TYR B 237 " pdb=" C TYR B 237 " pdb=" N ASN B 238 " pdb=" CA ASN B 238 " ideal model delta harmonic sigma weight residual -180.00 -159.88 -20.12 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 3621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 671 0.041 - 0.083: 237 0.083 - 0.124: 74 0.124 - 0.166: 21 0.166 - 0.207: 12 Chirality restraints: 1015 Sorted by residual: chirality pdb=" CA ASN B 478 " pdb=" N ASN B 478 " pdb=" C ASN B 478 " pdb=" CB ASN B 478 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA CYS B 210 " pdb=" N CYS B 210 " pdb=" C CYS B 210 " pdb=" CB CYS B 210 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ASP B 415 " pdb=" N ASP B 415 " pdb=" C ASP B 415 " pdb=" CB ASP B 415 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1012 not shown) Planarity restraints: 953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 487 " -0.060 2.00e-02 2.50e+03 4.49e-02 3.02e+01 pdb=" CG HIS B 487 " 0.061 2.00e-02 2.50e+03 pdb=" ND1 HIS B 487 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 HIS B 487 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 HIS B 487 " -0.039 2.00e-02 2.50e+03 pdb=" NE2 HIS B 487 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 229 " -0.053 2.00e-02 2.50e+03 4.01e-02 2.41e+01 pdb=" CG HIS B 229 " 0.054 2.00e-02 2.50e+03 pdb=" ND1 HIS B 229 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS B 229 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS B 229 " -0.037 2.00e-02 2.50e+03 pdb=" NE2 HIS B 229 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 83 " 0.044 2.00e-02 2.50e+03 3.24e-02 1.58e+01 pdb=" CG HIS A 83 " -0.047 2.00e-02 2.50e+03 pdb=" ND1 HIS A 83 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS A 83 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 HIS A 83 " 0.028 2.00e-02 2.50e+03 pdb=" NE2 HIS A 83 " 0.019 2.00e-02 2.50e+03 ... (remaining 950 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 510 2.72 - 3.27: 5827 3.27 - 3.81: 10466 3.81 - 4.36: 12799 4.36 - 4.90: 20376 Nonbonded interactions: 49978 Sorted by model distance: nonbonded pdb=" OD1 ASP B 90 " pdb="MG MG B 602 " model vdw 2.180 2.170 nonbonded pdb=" OD2 ASP B 90 " pdb="MG MG B 601 " model vdw 2.216 2.170 nonbonded pdb=" O ILE B 80 " pdb=" OH TYR B 296 " model vdw 2.221 2.440 nonbonded pdb=" OG SER B 171 " pdb=" O TRP B 227 " model vdw 2.226 2.440 nonbonded pdb=" OE1 GLU B 302 " pdb=" ND2 ASN B 422 " model vdw 2.257 2.520 ... (remaining 49973 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: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 49 5.49 5 Mg 2 5.21 5 S 52 5.16 5 C 3685 2.51 5 N 1033 2.21 5 O 1262 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 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.030 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.050 Process input model: 23.980 Find NCS groups from input model: 0.150 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 : 0.009 0.082 6339 Z= 0.571 Angle : 0.996 9.085 8841 Z= 0.611 Chirality : 0.052 0.207 1015 Planarity : 0.007 0.059 953 Dihedral : 13.783 171.703 2420 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.27), residues: 638 helix: -3.43 (0.29), residues: 142 sheet: -2.66 (0.62), residues: 49 loop : -2.34 (0.25), residues: 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2122 time to fit residues: 28.7618 Evaluate side-chains 84 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.667 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 0.0010 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 6339 Z= 0.195 Angle : 0.528 5.813 8841 Z= 0.276 Chirality : 0.039 0.150 1015 Planarity : 0.005 0.073 953 Dihedral : 10.345 172.943 1275 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.29), residues: 638 helix: -2.11 (0.37), residues: 148 sheet: -2.44 (0.63), residues: 46 loop : -1.81 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.651 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 104 average time/residue: 0.1749 time to fit residues: 24.2214 Evaluate side-chains 91 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1083 time to fit residues: 1.9637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.0670 chunk 17 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.0370 chunk 49 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 overall best weight: 0.1974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN B 108 GLN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 6339 Z= 0.144 Angle : 0.490 5.687 8841 Z= 0.252 Chirality : 0.038 0.145 1015 Planarity : 0.005 0.071 953 Dihedral : 10.137 173.245 1275 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.31), residues: 638 helix: -1.50 (0.40), residues: 155 sheet: -2.04 (0.64), residues: 48 loop : -1.49 (0.28), residues: 435 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.653 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 104 average time/residue: 0.1552 time to fit residues: 22.1728 Evaluate side-chains 92 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0556 time to fit residues: 1.2577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.1980 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 41 optimal weight: 0.0010 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 54 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 6339 Z= 0.157 Angle : 0.487 5.255 8841 Z= 0.251 Chirality : 0.039 0.149 1015 Planarity : 0.004 0.073 953 Dihedral : 10.021 173.408 1275 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.31), residues: 638 helix: -1.18 (0.42), residues: 150 sheet: -2.01 (0.59), residues: 60 loop : -1.29 (0.29), residues: 428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.671 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 99 average time/residue: 0.1449 time to fit residues: 20.1820 Evaluate side-chains 93 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.640 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0581 time to fit residues: 1.4889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS B 334 ASN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.106 6339 Z= 0.664 Angle : 0.726 6.848 8841 Z= 0.382 Chirality : 0.048 0.195 1015 Planarity : 0.006 0.084 953 Dihedral : 10.360 171.333 1275 Min Nonbonded Distance : 1.074 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.31), residues: 638 helix: -1.48 (0.42), residues: 148 sheet: -2.24 (0.54), residues: 68 loop : -1.59 (0.28), residues: 422 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.657 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 95 average time/residue: 0.1546 time to fit residues: 20.6021 Evaluate side-chains 92 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.689 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0625 time to fit residues: 2.0087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 7 optimal weight: 0.0070 chunk 37 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 6339 Z= 0.197 Angle : 0.525 6.694 8841 Z= 0.274 Chirality : 0.040 0.182 1015 Planarity : 0.005 0.089 953 Dihedral : 10.205 171.097 1275 Min Nonbonded Distance : 1.127 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.32), residues: 638 helix: -1.13 (0.42), residues: 149 sheet: -2.14 (0.59), residues: 54 loop : -1.32 (0.29), residues: 435 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.659 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 95 average time/residue: 0.1648 time to fit residues: 21.5330 Evaluate side-chains 91 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0572 time to fit residues: 1.2006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 55 optimal weight: 0.0980 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 41 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 6339 Z= 0.189 Angle : 0.508 8.989 8841 Z= 0.263 Chirality : 0.040 0.176 1015 Planarity : 0.005 0.082 953 Dihedral : 10.071 172.429 1275 Min Nonbonded Distance : 1.137 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.32), residues: 638 helix: -0.92 (0.43), residues: 149 sheet: -1.98 (0.58), residues: 54 loop : -1.15 (0.30), residues: 435 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.659 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 93 average time/residue: 0.1509 time to fit residues: 19.7362 Evaluate side-chains 89 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.650 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0566 time to fit residues: 1.0627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 6339 Z= 0.223 Angle : 0.534 13.921 8841 Z= 0.272 Chirality : 0.041 0.177 1015 Planarity : 0.004 0.068 953 Dihedral : 10.035 172.537 1275 Min Nonbonded Distance : 1.111 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.32), residues: 638 helix: -0.84 (0.42), residues: 149 sheet: -2.28 (0.52), residues: 74 loop : -0.96 (0.31), residues: 415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.678 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 93 average time/residue: 0.1540 time to fit residues: 20.1220 Evaluate side-chains 90 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.590 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0609 time to fit residues: 1.0174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 6339 Z= 0.202 Angle : 0.529 11.693 8841 Z= 0.267 Chirality : 0.040 0.176 1015 Planarity : 0.004 0.074 953 Dihedral : 9.989 172.909 1275 Min Nonbonded Distance : 1.132 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.32), residues: 638 helix: -0.73 (0.43), residues: 149 sheet: -1.71 (0.61), residues: 48 loop : -1.03 (0.30), residues: 441 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.632 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 88 average time/residue: 0.1609 time to fit residues: 19.9435 Evaluate side-chains 89 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.654 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0614 time to fit residues: 1.1082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 395 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 6339 Z= 0.323 Angle : 0.604 13.951 8841 Z= 0.303 Chirality : 0.042 0.189 1015 Planarity : 0.005 0.067 953 Dihedral : 10.041 172.520 1275 Min Nonbonded Distance : 1.081 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.32), residues: 638 helix: -0.89 (0.42), residues: 149 sheet: -1.92 (0.58), residues: 62 loop : -1.02 (0.30), residues: 427 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.683 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 83 average time/residue: 0.1602 time to fit residues: 18.7517 Evaluate side-chains 83 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.653 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0611 time to fit residues: 1.0730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.7980 chunk 54 optimal weight: 0.0870 chunk 22 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 ASN B 395 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.179743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.124085 restraints weight = 7391.893| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.05 r_work: 0.3428 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work: 0.3384 rms_B_bonded: 2.77 restraints_weight: 0.1250 r_work: 0.3363 rms_B_bonded: 2.89 restraints_weight: 0.0625 r_work: 0.3340 rms_B_bonded: 3.06 restraints_weight: 0.0312 r_work: 0.3316 rms_B_bonded: 3.27 restraints_weight: 0.0156 r_work: 0.3290 rms_B_bonded: 3.54 restraints_weight: 0.0078 r_work: 0.3262 rms_B_bonded: 3.86 restraints_weight: 0.0039 r_work: 0.3232 rms_B_bonded: 4.24 restraints_weight: 0.0020 r_work: 0.3200 rms_B_bonded: 4.68 restraints_weight: 0.0010 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 6339 Z= 0.217 Angle : 0.568 15.938 8841 Z= 0.281 Chirality : 0.040 0.184 1015 Planarity : 0.004 0.061 953 Dihedral : 10.010 172.785 1275 Min Nonbonded Distance : 1.108 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.33), residues: 638 helix: -0.90 (0.42), residues: 149 sheet: -1.88 (0.60), residues: 49 loop : -0.91 (0.30), residues: 440 =============================================================================== Job complete usr+sys time: 1438.57 seconds wall clock time: 26 minutes 55.39 seconds (1615.39 seconds total)