Starting phenix.real_space_refine (version: dev) on Fri Feb 17 21:05:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrh_21368/02_2023/6vrh_21368_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrh_21368/02_2023/6vrh_21368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrh_21368/02_2023/6vrh_21368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrh_21368/02_2023/6vrh_21368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrh_21368/02_2023/6vrh_21368_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrh_21368/02_2023/6vrh_21368_updated.pdb" } resolution = 3.3 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= 0.946 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 92 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "C ASP 37": "OD1" <-> "OD2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 6142 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4311 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 517} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "B" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 924 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 88 Unusual residues: {' CL': 1, '8PR': 1, 'LMT': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.25, per 1000 atoms: 0.69 Number of scatterers: 6142 At special positions: 0 Unit cell: (96.552, 103.032, 81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 F 1 9.00 O 1103 8.00 N 958 7.00 C 4045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " 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 NAG-ASN " NAG A 701 " - " ASN A 208 " " NAG A 704 " - " ASN A 217 " Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 4 sheets defined 49.6% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 85 through 96 removed outlier: 3.619A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.682A pdb=" N LEU A 119 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Proline residue: A 120 - end of helix removed outlier: 3.825A pdb=" N PHE A 127 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 143 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 156 through 189 removed outlier: 3.727A pdb=" N LYS A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLY A 160 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR A 176 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN A 177 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 179 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 274 through 284 removed outlier: 4.155A pdb=" N LYS A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 357 through 389 removed outlier: 3.688A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 397 No H-bonds generated for 'chain 'A' and resid 394 through 397' Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 409 through 416 Processing helix chain 'A' and resid 420 through 453 removed outlier: 3.943A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 4.570A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 495 Processing helix chain 'A' and resid 498 through 513 Processing helix chain 'A' and resid 518 through 529 Processing helix chain 'A' and resid 535 through 542 Processing helix chain 'A' and resid 544 through 558 Processing helix chain 'A' and resid 572 through 597 removed outlier: 4.045A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N CYS A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) Proline residue: A 590 - end of helix removed outlier: 4.667A pdb=" N LEU A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 611 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.960A pdb=" N ASP C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 108 through 110 removed outlier: 3.523A pdb=" N ILE C 68 " --> pdb=" O TRP C 55 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLN C 57 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU C 66 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 23 through 25 Processing sheet with id= D, first strand: chain 'B' and resid 54 through 58 removed outlier: 4.012A pdb=" N TYR B 127 " --> pdb=" O ARG B 117 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 693 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: 1.74 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1812 1.34 - 1.46: 1621 1.46 - 1.58: 2844 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6326 Sorted by residual: bond pdb=" CAT 8PR A 702 " pdb=" CAX 8PR A 702 " ideal model delta sigma weight residual 1.509 1.570 -0.061 2.00e-02 2.50e+03 9.45e+00 bond pdb=" CAV 8PR A 702 " pdb=" OAQ 8PR A 702 " ideal model delta sigma weight residual 1.354 1.413 -0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" CAI 8PR A 702 " pdb=" NAN 8PR A 702 " ideal model delta sigma weight residual 1.452 1.504 -0.052 2.00e-02 2.50e+03 6.79e+00 bond pdb=" CAU 8PR A 702 " pdb=" OAP 8PR A 702 " ideal model delta sigma weight residual 1.362 1.413 -0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" CAK 8PR A 702 " pdb=" NAN 8PR A 702 " ideal model delta sigma weight residual 1.451 1.498 -0.047 2.00e-02 2.50e+03 5.56e+00 ... (remaining 6321 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.63: 181 106.63 - 113.48: 3393 113.48 - 120.32: 2404 120.32 - 127.17: 2553 127.17 - 134.01: 88 Bond angle restraints: 8619 Sorted by residual: angle pdb=" CAE 8PR A 702 " pdb=" CAT 8PR A 702 " pdb=" CAX 8PR A 702 " ideal model delta sigma weight residual 120.67 109.67 11.00 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N ARG B 121 " pdb=" CA ARG B 121 " pdb=" C ARG B 121 " ideal model delta sigma weight residual 109.81 117.41 -7.60 2.21e+00 2.05e-01 1.18e+01 angle pdb=" CAF 8PR A 702 " pdb=" CAT 8PR A 702 " pdb=" CAX 8PR A 702 " ideal model delta sigma weight residual 121.28 130.08 -8.80 3.00e+00 1.11e-01 8.60e+00 angle pdb=" C VAL B 120 " pdb=" N ARG B 121 " pdb=" CA ARG B 121 " ideal model delta sigma weight residual 121.80 128.55 -6.75 2.44e+00 1.68e-01 7.64e+00 angle pdb=" C PRO B 122 " pdb=" N TYR B 123 " pdb=" CA TYR B 123 " ideal model delta sigma weight residual 122.82 126.45 -3.63 1.42e+00 4.96e-01 6.54e+00 ... (remaining 8614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3264 17.96 - 35.92: 285 35.92 - 53.88: 38 53.88 - 71.83: 3 71.83 - 89.79: 2 Dihedral angle restraints: 3592 sinusoidal: 1378 harmonic: 2214 Sorted by residual: dihedral pdb=" CA ARG B 121 " pdb=" C ARG B 121 " pdb=" N PRO B 122 " pdb=" CA PRO B 122 " ideal model delta harmonic sigma weight residual 180.00 129.71 50.29 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CB GLU A 78 " pdb=" CG GLU A 78 " pdb=" CD GLU A 78 " pdb=" OE1 GLU A 78 " ideal model delta sinusoidal sigma weight residual 0.00 89.79 -89.79 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA THR A 497 " pdb=" C THR A 497 " pdb=" N GLY A 498 " pdb=" CA GLY A 498 " ideal model delta harmonic sigma weight residual -180.00 -165.11 -14.89 0 5.00e+00 4.00e-02 8.86e+00 ... (remaining 3589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 722 0.042 - 0.083: 199 0.083 - 0.125: 43 0.125 - 0.166: 1 0.166 - 0.208: 1 Chirality restraints: 966 Sorted by residual: chirality pdb=" CAX 8PR A 702 " pdb=" CAJ 8PR A 702 " pdb=" CAT 8PR A 702 " pdb=" CAW 8PR A 702 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 217 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 963 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 121 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO B 122 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 287 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.21e+00 pdb=" N PRO A 288 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 130 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO A 131 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " 0.015 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 746 2.75 - 3.29: 6294 3.29 - 3.82: 10404 3.82 - 4.36: 11943 4.36 - 4.90: 20882 Nonbonded interactions: 50269 Sorted by model distance: nonbonded pdb=" O PRO A 571 " pdb=" OG SER A 574 " model vdw 2.212 2.440 nonbonded pdb=" OG SER A 242 " pdb=" O LEU A 248 " model vdw 2.242 2.440 nonbonded pdb=" OH TYR C 56 " pdb=" OE1 GLN C 109 " model vdw 2.265 2.440 nonbonded pdb=" OD1 ASP A 328 " pdb=" O4' LMT A 705 " model vdw 2.287 2.440 nonbonded pdb=" OG1 THR C 83 " pdb=" OG1 THR C 94 " model vdw 2.307 2.440 ... (remaining 50264 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 C 4045 2.51 5 N 958 2.21 5 O 1103 1.98 5 F 1 1.80 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 13.390 Check model and map are aligned: 0.090 Process input model: 20.960 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 40.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 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 : 0.003 0.061 6326 Z= 0.192 Angle : 0.543 11.004 8619 Z= 0.279 Chirality : 0.038 0.208 966 Planarity : 0.004 0.073 1048 Dihedral : 12.916 89.792 2177 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -3.01 (0.27), residues: 758 helix: -1.15 (0.24), residues: 360 sheet: -2.83 (0.43), residues: 105 loop : -2.61 (0.33), residues: 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1936 time to fit residues: 28.2295 Evaluate side-chains 88 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.0060 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 111 GLN A 112 ASN A 235 HIS C 26 GLN C 47 GLN C 57 GLN B 54 ASN B 69 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6326 Z= 0.177 Angle : 0.529 8.795 8619 Z= 0.275 Chirality : 0.039 0.136 966 Planarity : 0.005 0.077 1048 Dihedral : 4.479 51.397 861 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.98 (0.29), residues: 758 helix: -0.19 (0.25), residues: 369 sheet: -2.25 (0.44), residues: 106 loop : -2.35 (0.35), residues: 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.796 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 87 average time/residue: 0.2093 time to fit residues: 24.5395 Evaluate side-chains 86 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0695 time to fit residues: 2.1281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 0.0070 chunk 73 optimal weight: 0.6980 chunk 60 optimal weight: 0.0470 chunk 67 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 6326 Z= 0.142 Angle : 0.495 7.440 8619 Z= 0.256 Chirality : 0.037 0.126 966 Planarity : 0.004 0.076 1048 Dihedral : 4.420 51.486 861 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.44 (0.30), residues: 758 helix: 0.18 (0.27), residues: 372 sheet: -1.74 (0.45), residues: 106 loop : -2.11 (0.35), residues: 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.756 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 88 average time/residue: 0.1915 time to fit residues: 22.9530 Evaluate side-chains 81 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.770 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0612 time to fit residues: 1.3242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 0.0170 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 6326 Z= 0.163 Angle : 0.500 7.753 8619 Z= 0.258 Chirality : 0.038 0.130 966 Planarity : 0.004 0.076 1048 Dihedral : 4.431 50.698 861 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.08 (0.30), residues: 758 helix: 0.39 (0.27), residues: 364 sheet: -1.35 (0.47), residues: 106 loop : -1.85 (0.36), residues: 288 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 82 average time/residue: 0.1792 time to fit residues: 20.0570 Evaluate side-chains 79 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0651 time to fit residues: 1.6144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN C 26 GLN B 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 6326 Z= 0.200 Angle : 0.517 8.015 8619 Z= 0.270 Chirality : 0.039 0.135 966 Planarity : 0.004 0.078 1048 Dihedral : 4.579 51.989 861 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.98 (0.30), residues: 758 helix: 0.41 (0.27), residues: 364 sheet: -1.26 (0.49), residues: 105 loop : -1.73 (0.36), residues: 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 0.1866 time to fit residues: 18.5033 Evaluate side-chains 70 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.725 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0637 time to fit residues: 1.3178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 6326 Z= 0.202 Angle : 0.521 9.128 8619 Z= 0.269 Chirality : 0.039 0.259 966 Planarity : 0.004 0.078 1048 Dihedral : 4.587 52.092 861 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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 (0.31), residues: 758 helix: 0.46 (0.27), residues: 364 sheet: -1.19 (0.50), residues: 106 loop : -1.61 (0.37), residues: 288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 78 average time/residue: 0.1957 time to fit residues: 20.7633 Evaluate side-chains 74 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0765 time to fit residues: 1.9438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 54 ASN B 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.094 6326 Z= 0.217 Angle : 0.549 16.027 8619 Z= 0.273 Chirality : 0.039 0.150 966 Planarity : 0.004 0.078 1048 Dihedral : 4.628 53.377 861 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.86 (0.31), residues: 758 helix: 0.40 (0.27), residues: 367 sheet: -1.06 (0.49), residues: 107 loop : -1.56 (0.38), residues: 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.744 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 78 average time/residue: 0.1888 time to fit residues: 20.2398 Evaluate side-chains 76 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.701 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0625 time to fit residues: 1.7485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 0.0000 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 0.0970 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN C 26 GLN B 54 ASN B 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 6326 Z= 0.171 Angle : 0.518 12.585 8619 Z= 0.260 Chirality : 0.038 0.130 966 Planarity : 0.004 0.076 1048 Dihedral : 4.518 51.771 861 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.69 (0.31), residues: 758 helix: 0.53 (0.27), residues: 366 sheet: -0.91 (0.50), residues: 106 loop : -1.52 (0.38), residues: 286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 79 average time/residue: 0.1830 time to fit residues: 19.7057 Evaluate side-chains 74 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0790 time to fit residues: 1.3973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.0570 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 0.0050 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.5112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 6326 Z= 0.171 Angle : 0.524 13.604 8619 Z= 0.262 Chirality : 0.038 0.156 966 Planarity : 0.004 0.077 1048 Dihedral : 4.481 51.669 861 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.79 (0.31), residues: 758 helix: 0.45 (0.27), residues: 372 sheet: -0.87 (0.51), residues: 105 loop : -1.64 (0.37), residues: 281 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.814 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 70 average time/residue: 0.1999 time to fit residues: 19.1993 Evaluate side-chains 66 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0693 time to fit residues: 1.1992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 6326 Z= 0.188 Angle : 0.535 12.395 8619 Z= 0.267 Chirality : 0.038 0.126 966 Planarity : 0.004 0.077 1048 Dihedral : 4.527 52.136 861 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.79 (0.31), residues: 758 helix: 0.41 (0.27), residues: 373 sheet: -0.84 (0.50), residues: 105 loop : -1.60 (0.38), residues: 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.764 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1980 time to fit residues: 18.7564 Evaluate side-chains 67 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.0470 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.192890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.171670 restraints weight = 7881.411| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.95 r_work: 0.3937 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.095 6326 Z= 0.170 Angle : 0.523 11.908 8619 Z= 0.262 Chirality : 0.038 0.123 966 Planarity : 0.004 0.077 1048 Dihedral : 4.480 51.681 861 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.69 (0.31), residues: 758 helix: 0.45 (0.27), residues: 378 sheet: -0.78 (0.51), residues: 105 loop : -1.52 (0.39), residues: 275 =============================================================================== Job complete usr+sys time: 1783.43 seconds wall clock time: 33 minutes 44.13 seconds (2024.13 seconds total)