Starting phenix.real_space_refine on Tue Feb 13 08:11:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnd_34911/02_2024/8hnd_34911_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnd_34911/02_2024/8hnd_34911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnd_34911/02_2024/8hnd_34911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnd_34911/02_2024/8hnd_34911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnd_34911/02_2024/8hnd_34911_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnd_34911/02_2024/8hnd_34911_updated.pdb" } resolution = 3.19 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= 0.002 sd= 0.122 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 2879 2.51 5 N 685 2.21 5 O 770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 466": "OD1" <-> "OD2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4370 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4304 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 19, 'TRANS': 540} Chain breaks: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'FY5': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.15, per 1000 atoms: 0.72 Number of scatterers: 4370 At special positions: 0 Unit cell: (56.852, 68.036, 103.452, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 770 8.00 N 685 7.00 C 2879 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.02 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.02 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 802 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 828.5 milliseconds 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1018 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 1 sheets defined 62.1% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 29 through 49 Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.641A pdb=" N ARG A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 85 removed outlier: 4.090A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 115 Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 166 through 169 Processing helix chain 'A' and resid 171 through 198 removed outlier: 3.538A pdb=" N THR A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Proline residue: A 187 - end of helix Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 205 through 230 removed outlier: 4.282A pdb=" N ILE A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 258 through 276 Proline residue: A 275 - end of helix Processing helix chain 'A' and resid 325 through 334 Processing helix chain 'A' and resid 336 through 366 removed outlier: 4.766A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 380 Processing helix chain 'A' and resid 382 through 399 Processing helix chain 'A' and resid 404 through 427 removed outlier: 3.538A pdb=" N LYS A 409 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 528 through 561 removed outlier: 3.948A pdb=" N TYR A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 597 removed outlier: 5.643A pdb=" N SER A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 572 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 580 " --> pdb=" O MET A 577 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 581 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 582 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY A 583 " --> pdb=" O ARG A 580 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 585 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 586 " --> pdb=" O GLY A 583 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA A 587 " --> pdb=" O GLY A 584 " (cutoff:3.500A) Proline residue: A 588 - end of helix removed outlier: 4.075A pdb=" N PHE A 591 " --> pdb=" O PRO A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 650 Processing sheet with id= A, first strand: chain 'A' and resid 473 through 475 238 hydrogen bonds defined for protein. 660 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: 1.16 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 669 1.32 - 1.44: 1283 1.44 - 1.57: 2474 1.57 - 1.69: 1 1.69 - 1.81: 52 Bond restraints: 4479 Sorted by residual: bond pdb=" CA LEU A 27 " pdb=" C LEU A 27 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.11e-02 8.12e+03 2.60e+01 bond pdb=" C SER A 630 " pdb=" O SER A 630 " ideal model delta sigma weight residual 1.237 1.196 0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" O22 FY5 A 801 " pdb=" S21 FY5 A 801 " ideal model delta sigma weight residual 1.461 1.527 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" O20 FY5 A 801 " pdb=" S21 FY5 A 801 " ideal model delta sigma weight residual 1.673 1.613 0.060 2.00e-02 2.50e+03 8.98e+00 bond pdb=" O23 FY5 A 801 " pdb=" S21 FY5 A 801 " ideal model delta sigma weight residual 1.458 1.399 0.059 2.00e-02 2.50e+03 8.70e+00 ... (remaining 4474 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.08: 91 105.08 - 112.29: 2259 112.29 - 119.51: 1348 119.51 - 126.73: 2325 126.73 - 133.94: 50 Bond angle restraints: 6073 Sorted by residual: angle pdb=" N LYS A 28 " pdb=" CA LYS A 28 " pdb=" C LYS A 28 " ideal model delta sigma weight residual 113.41 103.39 10.02 1.22e+00 6.72e-01 6.74e+01 angle pdb=" N GLN A 369 " pdb=" CA GLN A 369 " pdb=" C GLN A 369 " ideal model delta sigma weight residual 109.64 118.36 -8.72 1.27e+00 6.20e-01 4.72e+01 angle pdb=" N GLU A 523 " pdb=" CA GLU A 523 " pdb=" C GLU A 523 " ideal model delta sigma weight residual 110.59 100.77 9.82 1.45e+00 4.76e-01 4.58e+01 angle pdb=" C PHE A 278 " pdb=" CA PHE A 278 " pdb=" CB PHE A 278 " ideal model delta sigma weight residual 111.51 101.08 10.43 1.58e+00 4.01e-01 4.36e+01 angle pdb=" N GLU A 60 " pdb=" CA GLU A 60 " pdb=" C GLU A 60 " ideal model delta sigma weight residual 111.52 120.47 -8.95 1.40e+00 5.10e-01 4.09e+01 ... (remaining 6068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.85: 2488 20.85 - 41.69: 154 41.69 - 62.54: 24 62.54 - 83.38: 1 83.38 - 104.23: 9 Dihedral angle restraints: 2676 sinusoidal: 1073 harmonic: 1603 Sorted by residual: dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -159.05 73.05 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS A 474 " pdb=" SG CYS A 474 " pdb=" SG CYS A 524 " pdb=" CB CYS A 524 " ideal model delta sinusoidal sigma weight residual 93.00 39.59 53.41 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" C CYS A 506 " pdb=" N CYS A 506 " pdb=" CA CYS A 506 " pdb=" CB CYS A 506 " ideal model delta harmonic sigma weight residual -122.60 -108.76 -13.84 0 2.50e+00 1.60e-01 3.07e+01 ... (remaining 2673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 668 0.126 - 0.252: 26 0.252 - 0.378: 7 0.378 - 0.504: 1 0.504 - 0.630: 3 Chirality restraints: 705 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 3.98e+01 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 516 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -3.03 0.63 2.00e-01 2.50e+01 9.93e+00 chirality pdb=" CA GLU A 60 " pdb=" N GLU A 60 " pdb=" C GLU A 60 " pdb=" CB GLU A 60 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.75e+00 ... (remaining 702 not shown) Planarity restraints: 737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.356 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG B 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.130 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.544 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 802 " 0.300 2.00e-02 2.50e+03 2.54e-01 8.06e+02 pdb=" C7 NAG A 802 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG A 802 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG A 802 " -0.438 2.00e-02 2.50e+03 pdb=" O7 NAG A 802 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.291 2.00e-02 2.50e+03 2.45e-01 7.53e+02 pdb=" C7 NAG B 2 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.420 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.022 2.00e-02 2.50e+03 ... (remaining 734 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1067 2.76 - 3.30: 4636 3.30 - 3.83: 7302 3.83 - 4.37: 8929 4.37 - 4.90: 14399 Nonbonded interactions: 36333 Sorted by model distance: nonbonded pdb=" O ILE A 595 " pdb=" OG1 THR A 598 " model vdw 2.231 2.440 nonbonded pdb=" O ASN A 403 " pdb=" N ILE A 407 " model vdw 2.310 2.520 nonbonded pdb=" NE2 GLN A 541 " pdb=" O23 FY5 A 801 " model vdw 2.370 2.520 nonbonded pdb=" O THR A 609 " pdb=" C ARG A 610 " model vdw 2.380 3.270 nonbonded pdb=" N GLU A 523 " pdb=" O GLU A 523 " model vdw 2.421 2.496 ... (remaining 36328 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.480 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.810 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 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 : 0.008 0.066 4479 Z= 0.496 Angle : 1.221 10.896 6073 Z= 0.803 Chirality : 0.074 0.630 705 Planarity : 0.018 0.306 735 Dihedral : 14.366 104.227 1637 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.65 % Allowed : 5.17 % Favored : 94.18 % Cbeta Deviations : 0.79 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.30), residues: 552 helix: -0.97 (0.25), residues: 351 sheet: None (None), residues: 0 loop : -3.32 (0.32), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 259 HIS 0.006 0.002 HIS A 451 PHE 0.012 0.001 PHE A 117 TYR 0.019 0.001 TYR A 590 ARG 0.004 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 38 PHE cc_start: 0.6996 (m-80) cc_final: 0.6754 (m-80) REVERT: A 48 MET cc_start: 0.7698 (tpt) cc_final: 0.7447 (tpt) REVERT: A 86 TYR cc_start: 0.6727 (t80) cc_final: 0.6460 (t80) REVERT: A 568 LYS cc_start: 0.7704 (tttt) cc_final: 0.6777 (tptt) REVERT: A 640 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7549 (t80) outliers start: 3 outliers final: 0 residues processed: 100 average time/residue: 0.1568 time to fit residues: 20.1134 Evaluate side-chains 76 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 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 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4479 Z= 0.216 Angle : 0.703 13.737 6073 Z= 0.330 Chirality : 0.043 0.242 705 Planarity : 0.005 0.040 735 Dihedral : 9.018 71.181 706 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.23 % Allowed : 11.42 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.34), residues: 552 helix: 0.68 (0.26), residues: 356 sheet: None (None), residues: 0 loop : -2.39 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 254 HIS 0.002 0.001 HIS A 204 PHE 0.019 0.001 PHE A 341 TYR 0.015 0.002 TYR A 442 ARG 0.002 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 118 MET cc_start: 0.8407 (ttm) cc_final: 0.7944 (mtp) REVERT: A 623 ARG cc_start: 0.7323 (ttt90) cc_final: 0.6392 (ttp-170) REVERT: A 640 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7604 (t80) outliers start: 15 outliers final: 10 residues processed: 81 average time/residue: 0.1430 time to fit residues: 15.3344 Evaluate side-chains 74 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4479 Z= 0.250 Angle : 0.623 10.898 6073 Z= 0.300 Chirality : 0.040 0.150 705 Planarity : 0.004 0.036 735 Dihedral : 7.158 73.018 706 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.02 % Allowed : 14.87 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.35), residues: 552 helix: 1.05 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -2.26 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 259 HIS 0.003 0.001 HIS A 520 PHE 0.019 0.001 PHE A 73 TYR 0.016 0.001 TYR A 590 ARG 0.002 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 338 TYR cc_start: 0.7583 (t80) cc_final: 0.7321 (t80) REVERT: A 623 ARG cc_start: 0.7461 (ttt90) cc_final: 0.6464 (ttp-170) REVERT: A 640 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7722 (t80) REVERT: A 649 LYS cc_start: 0.8013 (tptt) cc_final: 0.6476 (mtpt) outliers start: 14 outliers final: 9 residues processed: 81 average time/residue: 0.1380 time to fit residues: 14.9659 Evaluate side-chains 82 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 0.0070 chunk 54 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4479 Z= 0.239 Angle : 0.606 14.321 6073 Z= 0.286 Chirality : 0.039 0.144 705 Planarity : 0.004 0.038 735 Dihedral : 6.755 72.886 706 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.45 % Allowed : 15.95 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.35), residues: 552 helix: 1.30 (0.27), residues: 345 sheet: None (None), residues: 0 loop : -2.09 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 259 HIS 0.002 0.001 HIS A 115 PHE 0.015 0.001 PHE A 175 TYR 0.016 0.001 TYR A 590 ARG 0.002 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 517 TYR cc_start: 0.6228 (m-80) cc_final: 0.5683 (m-10) REVERT: A 623 ARG cc_start: 0.7396 (ttt90) cc_final: 0.6404 (ttp-170) REVERT: A 640 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.7701 (t80) outliers start: 16 outliers final: 10 residues processed: 81 average time/residue: 0.1315 time to fit residues: 14.4626 Evaluate side-chains 76 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.0670 chunk 46 optimal weight: 0.4980 chunk 37 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 31 optimal weight: 0.3980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4479 Z= 0.155 Angle : 0.559 10.035 6073 Z= 0.268 Chirality : 0.038 0.115 705 Planarity : 0.004 0.037 735 Dihedral : 6.594 71.654 706 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.02 % Allowed : 16.59 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.36), residues: 552 helix: 1.56 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.77 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 259 HIS 0.002 0.001 HIS A 92 PHE 0.014 0.001 PHE A 73 TYR 0.016 0.001 TYR A 590 ARG 0.002 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8553 (mtp) cc_final: 0.8106 (mtp) REVERT: A 217 MET cc_start: 0.8270 (mmt) cc_final: 0.7710 (mmt) REVERT: A 517 TYR cc_start: 0.6202 (m-80) cc_final: 0.5730 (m-10) REVERT: A 557 MET cc_start: 0.7965 (ttm) cc_final: 0.7708 (mtp) REVERT: A 623 ARG cc_start: 0.7437 (ttt90) cc_final: 0.6512 (ttp-170) REVERT: A 640 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7781 (t80) outliers start: 14 outliers final: 13 residues processed: 76 average time/residue: 0.1365 time to fit residues: 13.9827 Evaluate side-chains 77 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 chunk 30 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4479 Z= 0.194 Angle : 0.554 10.173 6073 Z= 0.267 Chirality : 0.038 0.116 705 Planarity : 0.004 0.039 735 Dihedral : 6.568 70.931 706 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.23 % Allowed : 17.24 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.36), residues: 552 helix: 1.65 (0.28), residues: 350 sheet: -3.03 (1.61), residues: 10 loop : -1.58 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 259 HIS 0.002 0.001 HIS A 115 PHE 0.025 0.001 PHE A 73 TYR 0.018 0.001 TYR A 442 ARG 0.001 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.8242 (mmt) cc_final: 0.7719 (mmt) REVERT: A 517 TYR cc_start: 0.6241 (m-80) cc_final: 0.5711 (m-10) REVERT: A 623 ARG cc_start: 0.7461 (ttt90) cc_final: 0.6572 (ttp-170) REVERT: A 640 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7773 (t80) outliers start: 15 outliers final: 12 residues processed: 77 average time/residue: 0.1344 time to fit residues: 14.0258 Evaluate side-chains 75 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4479 Z= 0.254 Angle : 0.587 11.371 6073 Z= 0.282 Chirality : 0.040 0.132 705 Planarity : 0.004 0.040 735 Dihedral : 6.572 70.737 706 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.09 % Allowed : 16.81 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.36), residues: 552 helix: 1.64 (0.27), residues: 346 sheet: -3.12 (1.55), residues: 10 loop : -1.56 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 602 HIS 0.003 0.001 HIS A 115 PHE 0.018 0.001 PHE A 73 TYR 0.018 0.001 TYR A 590 ARG 0.002 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 63 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 TYR cc_start: 0.6323 (m-80) cc_final: 0.5906 (m-10) REVERT: A 557 MET cc_start: 0.7977 (ttm) cc_final: 0.7673 (mtp) REVERT: A 623 ARG cc_start: 0.7438 (ttt90) cc_final: 0.6500 (ttp-170) REVERT: A 640 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7782 (t80) outliers start: 19 outliers final: 15 residues processed: 76 average time/residue: 0.1278 time to fit residues: 13.2604 Evaluate side-chains 76 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4479 Z= 0.197 Angle : 0.549 8.504 6073 Z= 0.270 Chirality : 0.039 0.123 705 Planarity : 0.004 0.039 735 Dihedral : 6.494 69.946 706 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.66 % Allowed : 17.46 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.36), residues: 552 helix: 1.67 (0.28), residues: 351 sheet: -2.79 (1.71), residues: 10 loop : -1.34 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 259 HIS 0.002 0.001 HIS A 115 PHE 0.018 0.001 PHE A 73 TYR 0.016 0.001 TYR A 590 ARG 0.001 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 MET cc_start: 0.8166 (mmt) cc_final: 0.7932 (tpp) REVERT: A 517 TYR cc_start: 0.6275 (m-80) cc_final: 0.5802 (m-10) REVERT: A 557 MET cc_start: 0.7990 (ttm) cc_final: 0.7708 (mtp) REVERT: A 623 ARG cc_start: 0.7438 (ttt90) cc_final: 0.6512 (ttp-170) REVERT: A 640 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.7673 (t80) outliers start: 17 outliers final: 14 residues processed: 75 average time/residue: 0.1354 time to fit residues: 13.6873 Evaluate side-chains 77 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 33 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 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 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4479 Z= 0.185 Angle : 0.543 8.473 6073 Z= 0.267 Chirality : 0.039 0.125 705 Planarity : 0.003 0.039 735 Dihedral : 6.431 68.982 706 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.02 % Allowed : 18.10 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.37), residues: 552 helix: 1.72 (0.28), residues: 351 sheet: -2.60 (1.86), residues: 10 loop : -1.17 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 259 HIS 0.002 0.001 HIS A 115 PHE 0.017 0.001 PHE A 73 TYR 0.016 0.001 TYR A 590 ARG 0.001 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.8138 (mmt) cc_final: 0.7675 (mmt) REVERT: A 517 TYR cc_start: 0.6210 (m-80) cc_final: 0.5759 (m-10) REVERT: A 557 MET cc_start: 0.7959 (ttm) cc_final: 0.7691 (mtp) REVERT: A 623 ARG cc_start: 0.7395 (ttt90) cc_final: 0.6484 (ttt180) REVERT: A 631 MET cc_start: 0.6547 (mtm) cc_final: 0.6258 (mtm) REVERT: A 640 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7666 (t80) outliers start: 14 outliers final: 11 residues processed: 75 average time/residue: 0.1381 time to fit residues: 13.9460 Evaluate side-chains 75 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4479 Z= 0.181 Angle : 0.536 8.452 6073 Z= 0.265 Chirality : 0.039 0.129 705 Planarity : 0.003 0.039 735 Dihedral : 6.395 68.241 706 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.80 % Allowed : 18.53 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.37), residues: 552 helix: 1.78 (0.28), residues: 351 sheet: -2.60 (1.87), residues: 10 loop : -1.07 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 259 HIS 0.002 0.001 HIS A 115 PHE 0.017 0.001 PHE A 73 TYR 0.016 0.001 TYR A 590 ARG 0.002 0.000 ARG A 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.8104 (mmt) cc_final: 0.7833 (mmt) REVERT: A 517 TYR cc_start: 0.6227 (m-80) cc_final: 0.5769 (m-10) REVERT: A 557 MET cc_start: 0.7960 (ttm) cc_final: 0.7701 (mtp) REVERT: A 623 ARG cc_start: 0.7411 (ttt90) cc_final: 0.6462 (ttt180) REVERT: A 640 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7666 (t80) outliers start: 13 outliers final: 12 residues processed: 75 average time/residue: 0.1451 time to fit residues: 14.4329 Evaluate side-chains 77 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.0770 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 0.0040 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.180249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.135235 restraints weight = 4782.164| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.16 r_work: 0.3380 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4479 Z= 0.168 Angle : 0.526 8.420 6073 Z= 0.261 Chirality : 0.038 0.133 705 Planarity : 0.003 0.039 735 Dihedral : 6.343 67.284 706 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.37 % Allowed : 18.97 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.37), residues: 552 helix: 1.86 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.11 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 259 HIS 0.002 0.001 HIS A 520 PHE 0.017 0.001 PHE A 73 TYR 0.016 0.001 TYR A 590 ARG 0.001 0.000 ARG A 526 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1278.93 seconds wall clock time: 23 minutes 46.26 seconds (1426.26 seconds total)