Starting phenix.real_space_refine on Mon Mar 11 00:21:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrh_21368/03_2024/6vrh_21368_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrh_21368/03_2024/6vrh_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_21368/03_2024/6vrh_21368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrh_21368/03_2024/6vrh_21368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrh_21368/03_2024/6vrh_21368_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrh_21368/03_2024/6vrh_21368_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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-5265/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.13, per 1000 atoms: 0.67 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: 2.45 Conformation dependent library (CDL) restraints added in 1.2 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: 1.19 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: 1.64 Time building geometry restraints manager: 2.65 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=" C2 LMT A 705 " pdb=" C3 LMT A 705 " pdb=" C4 LMT A 705 " ideal model delta sigma weight residual 117.09 107.26 9.83 3.00e+00 1.11e-01 1.07e+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=" C10 LMT A 705 " pdb=" C9 LMT A 705 " pdb=" C8 LMT A 705 " ideal model delta sigma weight residual 116.03 107.37 8.66 3.00e+00 1.11e-01 8.33e+00 ... (remaining 8614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.14: 3574 29.14 - 58.27: 111 58.27 - 87.41: 2 87.41 - 116.54: 1 116.54 - 145.68: 1 Dihedral angle restraints: 3689 sinusoidal: 1475 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=" CAX 8PR A 702 " pdb=" CAM 8PR A 702 " pdb=" CAW 8PR A 702 " pdb=" OAO 8PR A 702 " ideal model delta sinusoidal sigma weight residual 182.60 36.92 145.68 1 3.00e+01 1.11e-03 1.95e+01 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 ... (remaining 3686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 727 0.043 - 0.085: 193 0.085 - 0.128: 41 0.128 - 0.171: 1 0.171 - 0.213: 4 Chirality restraints: 966 Sorted by residual: chirality pdb=" C5' LMT A 705 " pdb=" C4' LMT A 705 " pdb=" C6' LMT A 705 " pdb=" O5' LMT A 705 " both_signs ideal model delta sigma weight residual False -2.51 -2.29 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C4' LMT A 705 " pdb=" C3' LMT A 705 " pdb=" C5' LMT A 705 " pdb=" O1B LMT A 705 " both_signs ideal model delta sigma weight residual False -2.55 -2.76 0.21 2.00e-01 2.50e+01 1.11e+00 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 ... (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 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 13.560 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.230 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6326 Z= 0.234 Angle : 0.604 11.004 8619 Z= 0.292 Chirality : 0.040 0.213 966 Planarity : 0.004 0.073 1048 Dihedral : 13.500 145.676 2274 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 % Allowed : 6.00 % Favored : 94.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 197 HIS 0.006 0.001 HIS C 111 PHE 0.013 0.001 PHE A 380 TYR 0.014 0.001 TYR B 123 ARG 0.002 0.000 ARG A 390 *********************** 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 : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.7829 (t80) cc_final: 0.7608 (t80) REVERT: A 270 ILE cc_start: 0.7191 (tp) cc_final: 0.6813 (tp) REVERT: A 271 TRP cc_start: 0.5986 (p-90) cc_final: 0.5554 (p-90) REVERT: A 272 LYS cc_start: 0.8402 (tppp) cc_final: 0.7912 (tptt) REVERT: A 311 PHE cc_start: 0.6600 (m-10) cc_final: 0.6390 (m-80) REVERT: A 316 ASN cc_start: 0.7477 (t0) cc_final: 0.6860 (t0) REVERT: A 615 GLU cc_start: 0.5133 (mp0) cc_final: 0.3315 (pt0) REVERT: C 62 GLN cc_start: 0.6892 (mm-40) cc_final: 0.6364 (mt0) REVERT: C 73 TYR cc_start: 0.8083 (m-80) cc_final: 0.7785 (m-80) REVERT: C 81 ARG cc_start: 0.6620 (tpm170) cc_final: 0.4840 (ptt90) REVERT: C 123 LYS cc_start: 0.6894 (mptt) cc_final: 0.6315 (mtpt) REVERT: B 39 ILE cc_start: 0.6117 (mm) cc_final: 0.5844 (tp) REVERT: B 57 LYS cc_start: 0.7771 (tttt) cc_final: 0.7131 (tttt) REVERT: B 130 GLN cc_start: 0.7601 (pt0) cc_final: 0.7401 (pt0) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1859 time to fit residues: 27.1313 Evaluate side-chains 91 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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: 0.4980 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 22 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 B 130 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6326 Z= 0.166 Angle : 0.516 8.769 8619 Z= 0.266 Chirality : 0.038 0.126 966 Planarity : 0.004 0.076 1048 Dihedral : 7.804 126.131 958 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.69 % Allowed : 10.92 % Favored : 87.38 % 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: -1.83 (0.29), residues: 758 helix: -0.05 (0.26), residues: 362 sheet: -2.31 (0.43), residues: 106 loop : -2.20 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 103 HIS 0.007 0.001 HIS C 111 PHE 0.015 0.001 PHE A 548 TYR 0.033 0.001 TYR A 142 ARG 0.003 0.000 ARG A 523 *********************** 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 94 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 176 TYR cc_start: 0.8053 (t80) cc_final: 0.7443 (t80) REVERT: A 204 TRP cc_start: 0.6705 (p90) cc_final: 0.6112 (p90) REVERT: A 270 ILE cc_start: 0.7194 (tp) cc_final: 0.6819 (tp) REVERT: A 271 TRP cc_start: 0.5994 (p-90) cc_final: 0.5571 (p-90) REVERT: A 272 LYS cc_start: 0.8526 (tppp) cc_final: 0.7778 (tptm) REVERT: A 316 ASN cc_start: 0.7475 (t0) cc_final: 0.6796 (t0) REVERT: A 600 THR cc_start: -0.0349 (OUTLIER) cc_final: -0.1474 (p) REVERT: A 615 GLU cc_start: 0.5141 (mp0) cc_final: 0.3278 (pt0) REVERT: C 62 GLN cc_start: 0.6874 (mm-40) cc_final: 0.6343 (mt0) REVERT: C 73 TYR cc_start: 0.8051 (m-80) cc_final: 0.7724 (m-80) REVERT: C 81 ARG cc_start: 0.6573 (tpm170) cc_final: 0.4772 (ptt90) REVERT: C 123 LYS cc_start: 0.6805 (mptt) cc_final: 0.6230 (mtpt) outliers start: 11 outliers final: 7 residues processed: 86 average time/residue: 0.1717 time to fit residues: 19.9808 Evaluate side-chains 89 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 68 optimal weight: 0.1980 chunk 73 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.6637 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6326 Z= 0.145 Angle : 0.493 7.716 8619 Z= 0.255 Chirality : 0.038 0.132 966 Planarity : 0.004 0.075 1048 Dihedral : 6.820 111.193 958 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.46 % Allowed : 12.46 % Favored : 85.08 % 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: -1.29 (0.30), residues: 758 helix: 0.30 (0.27), residues: 364 sheet: -1.69 (0.46), residues: 106 loop : -1.98 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 103 HIS 0.004 0.001 HIS C 111 PHE 0.029 0.001 PHE A 311 TYR 0.022 0.001 TYR A 142 ARG 0.003 0.000 ARG A 307 *********************** 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 98 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 204 TRP cc_start: 0.6691 (p90) cc_final: 0.6107 (p90) REVERT: A 270 ILE cc_start: 0.7176 (tp) cc_final: 0.6821 (tp) REVERT: A 271 TRP cc_start: 0.6039 (p-90) cc_final: 0.5574 (p-90) REVERT: A 272 LYS cc_start: 0.8447 (tppp) cc_final: 0.7743 (tptm) REVERT: A 316 ASN cc_start: 0.7485 (t0) cc_final: 0.6751 (t0) REVERT: A 600 THR cc_start: -0.0478 (OUTLIER) cc_final: -0.1481 (p) REVERT: A 615 GLU cc_start: 0.5200 (mp0) cc_final: 0.4950 (mm-30) REVERT: C 62 GLN cc_start: 0.6869 (mm-40) cc_final: 0.6360 (mt0) REVERT: C 73 TYR cc_start: 0.8115 (m-80) cc_final: 0.7784 (m-80) REVERT: C 81 ARG cc_start: 0.6619 (tpm170) cc_final: 0.4815 (ptt90) REVERT: C 123 LYS cc_start: 0.6779 (mptt) cc_final: 0.6212 (mtpt) outliers start: 16 outliers final: 11 residues processed: 89 average time/residue: 0.1787 time to fit residues: 21.4295 Evaluate side-chains 89 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6326 Z= 0.225 Angle : 0.536 8.108 8619 Z= 0.278 Chirality : 0.039 0.138 966 Planarity : 0.004 0.079 1048 Dihedral : 6.295 94.780 958 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.46 % Allowed : 14.92 % Favored : 82.62 % 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: -1.16 (0.30), residues: 758 helix: 0.29 (0.27), residues: 362 sheet: -1.33 (0.47), residues: 106 loop : -1.84 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 103 HIS 0.007 0.001 HIS C 111 PHE 0.042 0.002 PHE A 311 TYR 0.018 0.002 TYR B 123 ARG 0.002 0.000 ARG A 307 *********************** 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 96 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 TYR cc_start: 0.6045 (t80) cc_final: 0.5791 (t80) REVERT: A 124 MET cc_start: 0.7477 (mmp) cc_final: 0.7060 (mmp) REVERT: A 204 TRP cc_start: 0.6805 (p90) cc_final: 0.6303 (p90) REVERT: A 270 ILE cc_start: 0.7262 (tp) cc_final: 0.6916 (tp) REVERT: A 271 TRP cc_start: 0.6096 (p-90) cc_final: 0.5655 (p-90) REVERT: A 272 LYS cc_start: 0.8587 (tppp) cc_final: 0.8045 (tptt) REVERT: A 316 ASN cc_start: 0.7542 (t0) cc_final: 0.6790 (t0) REVERT: A 507 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6834 (tt) REVERT: A 615 GLU cc_start: 0.5415 (mp0) cc_final: 0.5043 (mm-30) REVERT: C 62 GLN cc_start: 0.6992 (mm-40) cc_final: 0.6385 (mt0) REVERT: C 73 TYR cc_start: 0.8308 (m-80) cc_final: 0.7724 (m-80) REVERT: C 81 ARG cc_start: 0.6615 (tpm170) cc_final: 0.4799 (ptt90) REVERT: C 123 LYS cc_start: 0.6848 (mptt) cc_final: 0.6269 (mtpt) outliers start: 16 outliers final: 14 residues processed: 85 average time/residue: 0.1787 time to fit residues: 20.6101 Evaluate side-chains 89 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 135 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 0.0570 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.0670 chunk 65 optimal weight: 0.0570 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.3354 ------------------------------------------------------------------------------- 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 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6326 Z= 0.130 Angle : 0.481 7.739 8619 Z= 0.249 Chirality : 0.037 0.129 966 Planarity : 0.004 0.075 1048 Dihedral : 5.738 79.012 958 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.62 % Allowed : 15.54 % Favored : 81.85 % 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 (0.30), residues: 758 helix: 0.54 (0.27), residues: 361 sheet: -1.18 (0.49), residues: 105 loop : -1.70 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 103 HIS 0.004 0.001 HIS C 111 PHE 0.030 0.001 PHE A 311 TYR 0.017 0.001 TYR B 123 ARG 0.002 0.000 ARG A 390 *********************** 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 97 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7513 (mmp) cc_final: 0.6986 (mmp) REVERT: A 135 MET cc_start: 0.8526 (ttp) cc_final: 0.8225 (ttp) REVERT: A 204 TRP cc_start: 0.6714 (p90) cc_final: 0.6166 (p90) REVERT: A 270 ILE cc_start: 0.7153 (tp) cc_final: 0.6798 (tp) REVERT: A 271 TRP cc_start: 0.6057 (p-90) cc_final: 0.5603 (p-90) REVERT: A 272 LYS cc_start: 0.8455 (tppp) cc_final: 0.7725 (tptm) REVERT: A 316 ASN cc_start: 0.7465 (t0) cc_final: 0.6688 (t0) REVERT: A 494 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8036 (mt-10) REVERT: A 507 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6726 (tt) REVERT: A 600 THR cc_start: -0.0303 (OUTLIER) cc_final: -0.1362 (p) REVERT: A 615 GLU cc_start: 0.5250 (mp0) cc_final: 0.4988 (mm-30) REVERT: C 62 GLN cc_start: 0.6914 (mm-40) cc_final: 0.6360 (mt0) REVERT: C 73 TYR cc_start: 0.8184 (m-80) cc_final: 0.7735 (m-80) REVERT: C 81 ARG cc_start: 0.6544 (tpm170) cc_final: 0.4834 (ptt90) REVERT: C 123 LYS cc_start: 0.6805 (mptt) cc_final: 0.6243 (mmmt) REVERT: B 79 TYR cc_start: 0.3859 (p90) cc_final: 0.3608 (p90) REVERT: B 123 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.5607 (t80) outliers start: 17 outliers final: 11 residues processed: 89 average time/residue: 0.1758 time to fit residues: 21.2983 Evaluate side-chains 89 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 6326 Z= 0.541 Angle : 0.729 8.458 8619 Z= 0.381 Chirality : 0.046 0.162 966 Planarity : 0.005 0.088 1048 Dihedral : 6.786 76.797 958 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 3.69 % Allowed : 16.62 % Favored : 79.69 % 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: -1.61 (0.29), residues: 758 helix: -0.45 (0.25), residues: 369 sheet: -1.24 (0.48), residues: 108 loop : -1.66 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 103 HIS 0.012 0.002 HIS C 111 PHE 0.047 0.003 PHE A 428 TYR 0.021 0.003 TYR B 46 ARG 0.005 0.001 ARG A 607 *********************** 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 105 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7211 (tmtt) cc_final: 0.6937 (tptm) REVERT: A 271 TRP cc_start: 0.6317 (p-90) cc_final: 0.5824 (p-90) REVERT: A 272 LYS cc_start: 0.8790 (tppp) cc_final: 0.8279 (tptp) REVERT: A 316 ASN cc_start: 0.7780 (t0) cc_final: 0.6999 (t0) REVERT: A 507 ILE cc_start: 0.7084 (OUTLIER) cc_final: 0.6860 (tt) REVERT: A 587 ILE cc_start: 0.8081 (tt) cc_final: 0.7770 (tp) REVERT: C 62 GLN cc_start: 0.7185 (mm-40) cc_final: 0.6472 (mt0) REVERT: C 75 TYR cc_start: 0.7988 (t80) cc_final: 0.7468 (t80) REVERT: C 81 ARG cc_start: 0.6620 (tpm170) cc_final: 0.4833 (ptt90) REVERT: C 123 LYS cc_start: 0.7095 (mptt) cc_final: 0.6451 (mtpt) REVERT: B 123 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7628 (t80) REVERT: B 130 GLN cc_start: 0.7867 (pt0) cc_final: 0.7182 (pt0) outliers start: 24 outliers final: 17 residues processed: 97 average time/residue: 0.1721 time to fit residues: 22.5941 Evaluate side-chains 97 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 126 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 0.1980 chunk 45 optimal weight: 0.0020 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 overall best weight: 0.3988 ------------------------------------------------------------------------------- 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: 0.6724 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 6326 Z= 0.172 Angle : 0.557 14.907 8619 Z= 0.282 Chirality : 0.041 0.280 966 Planarity : 0.004 0.079 1048 Dihedral : 6.042 68.525 958 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.38 % Allowed : 18.46 % Favored : 78.15 % 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: -0.97 (0.31), residues: 758 helix: 0.20 (0.27), residues: 362 sheet: -1.00 (0.50), residues: 107 loop : -1.48 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 103 HIS 0.005 0.001 HIS C 111 PHE 0.032 0.001 PHE A 428 TYR 0.018 0.001 TYR B 123 ARG 0.003 0.000 ARG A 390 *********************** 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 97 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.8639 (ttp) cc_final: 0.8300 (ttp) REVERT: A 241 ARG cc_start: 0.7905 (mtp180) cc_final: 0.7645 (mtp180) REVERT: A 272 LYS cc_start: 0.8713 (tppp) cc_final: 0.8470 (tptp) REVERT: A 316 ASN cc_start: 0.7514 (t0) cc_final: 0.6717 (t0) REVERT: A 383 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5782 (mp) REVERT: A 507 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6794 (tt) REVERT: A 615 GLU cc_start: 0.5660 (mp0) cc_final: 0.5147 (mp0) REVERT: C 62 GLN cc_start: 0.6909 (mm-40) cc_final: 0.6238 (mt0) REVERT: C 81 ARG cc_start: 0.6607 (tpm170) cc_final: 0.4865 (ptt90) REVERT: C 123 LYS cc_start: 0.6914 (mptt) cc_final: 0.6346 (mtpt) REVERT: B 79 TYR cc_start: 0.3840 (p90) cc_final: 0.3587 (p90) REVERT: B 123 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.5826 (t80) REVERT: B 130 GLN cc_start: 0.7842 (pt0) cc_final: 0.7172 (pt0) outliers start: 22 outliers final: 15 residues processed: 89 average time/residue: 0.1712 time to fit residues: 20.6722 Evaluate side-chains 90 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 126 ASP 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: 4.9990 chunk 45 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 65 optimal weight: 0.0770 chunk 69 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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: 0.6695 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 0.070 6326 Z= 0.163 Angle : 0.524 11.056 8619 Z= 0.267 Chirality : 0.039 0.245 966 Planarity : 0.004 0.080 1048 Dihedral : 5.810 61.331 958 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.92 % Allowed : 18.77 % Favored : 78.31 % 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: -0.74 (0.31), residues: 758 helix: 0.46 (0.27), residues: 363 sheet: -0.95 (0.51), residues: 105 loop : -1.45 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 103 HIS 0.004 0.001 HIS C 111 PHE 0.034 0.001 PHE A 311 TYR 0.020 0.001 TYR C 75 ARG 0.002 0.000 ARG A 241 *********************** 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 94 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8581 (ttp) cc_final: 0.8246 (ttp) REVERT: A 272 LYS cc_start: 0.8619 (tppp) cc_final: 0.8413 (tptp) REVERT: A 316 ASN cc_start: 0.7549 (t0) cc_final: 0.6762 (t0) REVERT: A 383 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5785 (mp) REVERT: A 440 PHE cc_start: 0.6308 (m-10) cc_final: 0.5774 (m-10) REVERT: A 507 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6773 (tt) REVERT: A 615 GLU cc_start: 0.5573 (mp0) cc_final: 0.5153 (mp0) REVERT: C 62 GLN cc_start: 0.6861 (mm-40) cc_final: 0.6293 (mt0) REVERT: C 81 ARG cc_start: 0.6610 (tpm170) cc_final: 0.4925 (ptt90) REVERT: C 123 LYS cc_start: 0.6907 (mptt) cc_final: 0.6358 (mtpt) REVERT: B 79 TYR cc_start: 0.3844 (p90) cc_final: 0.3597 (p90) REVERT: B 123 TYR cc_start: 0.7420 (OUTLIER) cc_final: 0.5737 (t80) REVERT: B 130 GLN cc_start: 0.7835 (pt0) cc_final: 0.7152 (pt0) outliers start: 19 outliers final: 14 residues processed: 85 average time/residue: 0.1692 time to fit residues: 19.6153 Evaluate side-chains 87 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 135 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 0.0670 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6326 Z= 0.183 Angle : 0.534 8.749 8619 Z= 0.274 Chirality : 0.040 0.228 966 Planarity : 0.004 0.079 1048 Dihedral : 5.793 58.820 958 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.92 % Allowed : 18.92 % Favored : 78.15 % 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: -0.74 (0.31), residues: 758 helix: 0.45 (0.27), residues: 363 sheet: -0.86 (0.51), residues: 105 loop : -1.48 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 103 HIS 0.005 0.001 HIS C 111 PHE 0.038 0.002 PHE A 428 TYR 0.020 0.001 TYR C 75 ARG 0.002 0.000 ARG A 390 *********************** 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 90 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8600 (ttp) cc_final: 0.8222 (ttp) REVERT: A 316 ASN cc_start: 0.7535 (t0) cc_final: 0.6743 (t0) REVERT: A 383 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5801 (mp) REVERT: A 507 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6788 (tt) REVERT: A 615 GLU cc_start: 0.5582 (mp0) cc_final: 0.5131 (mp0) REVERT: C 62 GLN cc_start: 0.6903 (mm-40) cc_final: 0.6347 (mt0) REVERT: C 81 ARG cc_start: 0.6612 (tpm170) cc_final: 0.4932 (ptt90) REVERT: C 123 LYS cc_start: 0.6914 (mptt) cc_final: 0.6347 (mtpt) REVERT: B 79 TYR cc_start: 0.3825 (p90) cc_final: 0.3580 (p90) REVERT: B 123 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.5783 (t80) REVERT: B 130 GLN cc_start: 0.7835 (pt0) cc_final: 0.7144 (pt0) outliers start: 19 outliers final: 14 residues processed: 82 average time/residue: 0.1775 time to fit residues: 19.7546 Evaluate side-chains 85 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 126 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6326 Z= 0.209 Angle : 0.546 8.050 8619 Z= 0.281 Chirality : 0.040 0.226 966 Planarity : 0.004 0.080 1048 Dihedral : 5.796 56.921 958 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.77 % Allowed : 19.23 % Favored : 78.00 % 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: -0.72 (0.31), residues: 758 helix: 0.43 (0.27), residues: 363 sheet: -0.79 (0.51), residues: 105 loop : -1.43 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 103 HIS 0.006 0.001 HIS C 111 PHE 0.038 0.002 PHE A 428 TYR 0.020 0.001 TYR C 75 ARG 0.002 0.000 ARG A 390 ********************** 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 86 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7359 (mmp) cc_final: 0.6955 (mmp) REVERT: A 135 MET cc_start: 0.8628 (ttp) cc_final: 0.8205 (ttp) REVERT: A 316 ASN cc_start: 0.7594 (t0) cc_final: 0.6808 (t0) REVERT: A 383 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5807 (mp) REVERT: A 507 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6803 (tt) REVERT: A 615 GLU cc_start: 0.5629 (mp0) cc_final: 0.5112 (mp0) REVERT: C 62 GLN cc_start: 0.6911 (mm-40) cc_final: 0.6353 (mt0) REVERT: C 81 ARG cc_start: 0.6578 (tpm170) cc_final: 0.4877 (ptt90) REVERT: C 123 LYS cc_start: 0.6941 (mptt) cc_final: 0.6379 (mtpt) REVERT: B 79 TYR cc_start: 0.3847 (p90) cc_final: 0.3605 (p90) REVERT: B 123 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.5750 (t80) REVERT: B 130 GLN cc_start: 0.7821 (pt0) cc_final: 0.7123 (pt0) outliers start: 18 outliers final: 15 residues processed: 78 average time/residue: 0.1836 time to fit residues: 19.7072 Evaluate side-chains 86 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 126 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.0870 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.0030 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.0570 chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 0.0770 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 overall best weight: 0.2044 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.200961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.180268 restraints weight = 7862.262| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.99 r_work: 0.3958 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 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 : 0.002 0.049 6326 Z= 0.133 Angle : 0.502 7.693 8619 Z= 0.258 Chirality : 0.038 0.218 966 Planarity : 0.004 0.077 1048 Dihedral : 5.361 53.477 958 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.85 % Allowed : 20.46 % Favored : 77.69 % 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: -0.50 (0.31), residues: 758 helix: 0.65 (0.27), residues: 363 sheet: -0.69 (0.52), residues: 105 loop : -1.38 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 103 HIS 0.002 0.001 HIS C 111 PHE 0.038 0.001 PHE A 311 TYR 0.017 0.001 TYR C 75 ARG 0.002 0.000 ARG A 390 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1804.34 seconds wall clock time: 33 minutes 23.76 seconds (2003.76 seconds total)