Starting phenix.real_space_refine on Tue Feb 13 14:08:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe6_22144/02_2024/6xe6_22144.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe6_22144/02_2024/6xe6_22144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe6_22144/02_2024/6xe6_22144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe6_22144/02_2024/6xe6_22144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe6_22144/02_2024/6xe6_22144.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe6_22144/02_2024/6xe6_22144.pdb" } resolution = 4.53 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= 0.000 sd= 0.003 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 54 5.16 5 C 4298 2.51 5 N 1022 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 373": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 573": "OD1" <-> "OD2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 579": "OD1" <-> "OD2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "A PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 700": "OE1" <-> "OE2" Residue "A PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 763": "NH1" <-> "NH2" Residue "A PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 864": "OD1" <-> "OD2" Residue "A PHE 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 892": "NH1" <-> "NH2" Residue "A ARG 921": "NH1" <-> "NH2" Residue "A GLU 938": "OE1" <-> "OE2" Residue "A GLU 946": "OE1" <-> "OE2" Residue "A GLU 960": "OE1" <-> "OE2" Residue "A PHE 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 975": "OD1" <-> "OD2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1061": "NH1" <-> "NH2" Residue "A ARG 1068": "NH1" <-> "NH2" 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: 6530 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6530 Unusual residues: {'NAG': 1, 'Y01': 5} Classifications: {'peptide': 826, 'undetermined': 6} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 36, 'TRANS': 789, None: 6} Not linked: pdbres="PRO A1144 " pdbres="Y01 A1301 " Not linked: pdbres="Y01 A1301 " pdbres="Y01 A1302 " Not linked: pdbres="Y01 A1302 " pdbres="Y01 A1303 " Not linked: pdbres="Y01 A1303 " pdbres="Y01 A1304 " Not linked: pdbres="Y01 A1304 " pdbres="Y01 A1305 " Not linked: pdbres="Y01 A1305 " pdbres="NAG A1306 " Chain breaks: 10 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 150 Time building chain proxies: 3.96, per 1000 atoms: 0.61 Number of scatterers: 6530 At special positions: 0 Unit cell: (99.96, 74.97, 119.119, 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 54 16.00 O 1156 8.00 N 1022 7.00 C 4298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 367 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.3 seconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 62.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 179 through 188 removed outlier: 3.547A pdb=" N TRP A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 210 Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.534A pdb=" N ASN A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 370 through 385 removed outlier: 4.701A pdb=" N CYS A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 432 removed outlier: 3.974A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'A' and resid 491 through 523 removed outlier: 4.545A pdb=" N GLN A 497 " --> pdb=" O HIS A 493 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU A 501 " --> pdb=" O GLN A 497 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N MET A 502 " --> pdb=" O ASP A 498 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Proline residue: A 507 - end of helix removed outlier: 3.527A pdb=" N LYS A 523 " --> pdb=" O CYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 549 removed outlier: 3.562A pdb=" N THR A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 570 removed outlier: 3.792A pdb=" N THR A 561 " --> pdb=" O PHE A 557 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A 563 " --> pdb=" O ASN A 559 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 569 " --> pdb=" O ILE A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 588 removed outlier: 3.713A pdb=" N PHE A 575 " --> pdb=" O ALA A 571 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP A 579 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 586 " --> pdb=" O ASN A 582 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 587 " --> pdb=" O TYR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 623 removed outlier: 3.617A pdb=" N THR A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE A 619 " --> pdb=" O THR A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 661 removed outlier: 3.827A pdb=" N ARG A 631 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 645 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) Proline residue: A 653 - end of helix Processing helix chain 'A' and resid 689 through 716 Proline residue: A 711 - end of helix Processing helix chain 'A' and resid 719 through 736 removed outlier: 3.874A pdb=" N PHE A 723 " --> pdb=" O TYR A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.659A pdb=" N ARG A 763 " --> pdb=" O HIS A 759 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP A 765 " --> pdb=" O PHE A 761 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA A 766 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 837 Processing helix chain 'A' and resid 852 through 862 removed outlier: 3.613A pdb=" N PHE A 856 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 896 Processing helix chain 'A' and resid 938 through 955 removed outlier: 3.558A pdb=" N GLN A 942 " --> pdb=" O GLU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 1003 removed outlier: 3.507A pdb=" N ASP A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1030 removed outlier: 3.569A pdb=" N GLY A1025 " --> pdb=" O PHE A1021 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A1028 " --> pdb=" O VAL A1024 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A1030 " --> pdb=" O SER A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1062 removed outlier: 3.987A pdb=" N HIS A1055 " --> pdb=" O ASP A1051 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A1059 " --> pdb=" O HIS A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1096 removed outlier: 4.625A pdb=" N MET A1085 " --> pdb=" O SER A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1134 removed outlier: 3.690A pdb=" N THR A1106 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA A1121 " --> pdb=" O CYS A1117 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS A1133 " --> pdb=" O CYS A1129 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1071 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: 2.00 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1050 1.33 - 1.45: 1802 1.45 - 1.57: 3758 1.57 - 1.70: 3 1.70 - 1.82: 85 Bond restraints: 6698 Sorted by residual: bond pdb=" CAX Y01 A1303 " pdb=" OAH Y01 A1303 " ideal model delta sigma weight residual 1.248 1.345 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" CAX Y01 A1304 " pdb=" OAH Y01 A1304 " ideal model delta sigma weight residual 1.248 1.344 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" CAX Y01 A1302 " pdb=" OAH Y01 A1302 " ideal model delta sigma weight residual 1.248 1.344 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" CAX Y01 A1305 " pdb=" OAH Y01 A1305 " ideal model delta sigma weight residual 1.248 1.344 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" CAX Y01 A1301 " pdb=" OAH Y01 A1301 " ideal model delta sigma weight residual 1.248 1.343 -0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 6693 not shown) Histogram of bond angle deviations from ideal: 98.09 - 105.29: 155 105.29 - 112.49: 3117 112.49 - 119.69: 2485 119.69 - 126.89: 3292 126.89 - 134.10: 89 Bond angle restraints: 9138 Sorted by residual: angle pdb=" C HIS A 759 " pdb=" N PRO A 760 " pdb=" CA PRO A 760 " ideal model delta sigma weight residual 119.84 130.49 -10.65 1.25e+00 6.40e-01 7.26e+01 angle pdb=" N PRO A 439 " pdb=" CA PRO A 439 " pdb=" CB PRO A 439 " ideal model delta sigma weight residual 103.25 111.16 -7.91 1.05e+00 9.07e-01 5.67e+01 angle pdb=" N PRO A 447 " pdb=" CA PRO A 447 " pdb=" CB PRO A 447 " ideal model delta sigma weight residual 103.00 110.09 -7.09 1.10e+00 8.26e-01 4.16e+01 angle pdb=" N PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta sigma weight residual 103.00 109.71 -6.71 1.10e+00 8.26e-01 3.72e+01 angle pdb=" N TYR A 300 " pdb=" CA TYR A 300 " pdb=" C TYR A 300 " ideal model delta sigma weight residual 111.03 117.61 -6.58 1.11e+00 8.12e-01 3.52e+01 ... (remaining 9133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 3725 17.13 - 34.26: 331 34.26 - 51.40: 102 51.40 - 68.53: 16 68.53 - 85.66: 2 Dihedral angle restraints: 4176 sinusoidal: 1753 harmonic: 2423 Sorted by residual: dihedral pdb=" CA LYS A 588 " pdb=" C LYS A 588 " pdb=" N PRO A 589 " pdb=" CA PRO A 589 " ideal model delta harmonic sigma weight residual -180.00 -150.51 -29.49 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CB CYS A 323 " pdb=" SG CYS A 323 " pdb=" SG CYS A 367 " pdb=" CB CYS A 367 " ideal model delta sinusoidal sigma weight residual 93.00 45.42 47.58 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CA ALA A1082 " pdb=" C ALA A1082 " pdb=" N MET A1083 " pdb=" CA MET A1083 " ideal model delta harmonic sigma weight residual -180.00 -153.97 -26.03 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 4173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 852 0.078 - 0.157: 179 0.157 - 0.235: 33 0.235 - 0.313: 7 0.313 - 0.392: 5 Chirality restraints: 1076 Sorted by residual: chirality pdb=" CBG Y01 A1303 " pdb=" CAQ Y01 A1303 " pdb=" CBD Y01 A1303 " pdb=" CBI Y01 A1303 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CBG Y01 A1305 " pdb=" CAQ Y01 A1305 " pdb=" CBD Y01 A1305 " pdb=" CBI Y01 A1305 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CBG Y01 A1304 " pdb=" CAQ Y01 A1304 " pdb=" CBD Y01 A1304 " pdb=" CBI Y01 A1304 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 1073 not shown) Planarity restraints: 1104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 879 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO A 880 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 880 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 880 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 876 " 0.022 2.00e-02 2.50e+03 1.94e-02 5.64e+00 pdb=" CG HIS A 876 " -0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS A 876 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS A 876 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS A 876 " 0.017 2.00e-02 2.50e+03 pdb=" NE2 HIS A 876 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 316 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO A 317 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 317 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 317 " 0.032 5.00e-02 4.00e+02 ... (remaining 1101 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 3 1.86 - 2.62: 42 2.62 - 3.38: 9038 3.38 - 4.14: 14438 4.14 - 4.90: 24894 Nonbonded interactions: 48415 Sorted by model distance: nonbonded pdb=" OD1 ASN A 836 " pdb=" O1 NAG A1306 " model vdw 1.098 2.440 nonbonded pdb=" O SER A 820 " pdb=" NE2 GLN A 883 " model vdw 1.733 2.520 nonbonded pdb=" O PRO A 910 " pdb=" O ALA A 922 " model vdw 1.773 3.040 nonbonded pdb=" CG ASN A 836 " pdb=" O1 NAG A1306 " model vdw 2.181 3.270 nonbonded pdb=" O VAL A 610 " pdb=" OG1 THR A 614 " model vdw 2.266 2.440 ... (remaining 48410 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 group one per residue 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: 0.750 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: 0.000 Extract box with map and model: 3.880 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.500 Find NCS groups from input model: 0.350 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: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 : 0.011 0.139 6698 Z= 0.688 Angle : 1.399 10.649 9138 Z= 0.913 Chirality : 0.072 0.392 1076 Planarity : 0.005 0.065 1104 Dihedral : 14.626 85.659 2597 Min Nonbonded Distance : 1.098 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 1.24 % Allowed : 11.32 % Favored : 87.44 % Rotamer: Outliers : 1.05 % Allowed : 10.38 % Favored : 88.57 % Cbeta Deviations : 0.25 % 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: -4.98 (0.22), residues: 804 helix: -2.36 (0.18), residues: 473 sheet: None (None), residues: 0 loop : -4.80 (0.25), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 826 HIS 0.017 0.002 HIS A 876 PHE 0.024 0.003 PHE A 839 TYR 0.019 0.002 TYR A 764 ARG 0.010 0.001 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 232 time to evaluate : 0.681 Fit side-chains REVERT: A 220 LEU cc_start: 0.9012 (pp) cc_final: 0.8792 (pp) REVERT: A 221 LEU cc_start: 0.9445 (tp) cc_final: 0.9056 (tp) REVERT: A 383 ARG cc_start: 0.7858 (mtt180) cc_final: 0.6452 (tpt-90) REVERT: A 433 ASP cc_start: 0.7709 (m-30) cc_final: 0.7436 (m-30) REVERT: A 453 MET cc_start: 0.5448 (pmm) cc_final: 0.4694 (pmm) REVERT: A 465 MET cc_start: 0.8420 (ttt) cc_final: 0.7961 (tpt) REVERT: A 573 ASP cc_start: 0.8357 (m-30) cc_final: 0.7791 (m-30) REVERT: A 578 CYS cc_start: 0.8937 (m) cc_final: 0.8595 (m) REVERT: A 581 TRP cc_start: 0.8950 (t-100) cc_final: 0.8185 (t-100) REVERT: A 597 VAL cc_start: 0.9693 (p) cc_final: 0.9402 (p) REVERT: A 620 TYR cc_start: 0.8790 (m-80) cc_final: 0.8158 (m-80) REVERT: A 796 GLU cc_start: 0.8965 (tt0) cc_final: 0.8686 (tt0) REVERT: A 798 ASN cc_start: 0.7981 (p0) cc_final: 0.7290 (t0) REVERT: A 889 CYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8387 (m) REVERT: A 970 ASN cc_start: 0.8277 (p0) cc_final: 0.8018 (p0) REVERT: A 1011 TYR cc_start: 0.8822 (m-10) cc_final: 0.6857 (m-80) REVERT: A 1029 LEU cc_start: 0.9265 (tp) cc_final: 0.9003 (tp) REVERT: A 1032 TRP cc_start: 0.7323 (OUTLIER) cc_final: 0.6775 (t60) REVERT: A 1034 LEU cc_start: 0.9423 (tt) cc_final: 0.8887 (mp) REVERT: A 1052 PHE cc_start: 0.8249 (m-80) cc_final: 0.8013 (m-80) REVERT: A 1083 MET cc_start: 0.8866 (mmp) cc_final: 0.8645 (mmm) REVERT: A 1101 THR cc_start: 0.9146 (m) cc_final: 0.8946 (m) REVERT: A 1112 MET cc_start: 0.8317 (ppp) cc_final: 0.7541 (ppp) outliers start: 7 outliers final: 2 residues processed: 236 average time/residue: 0.1534 time to fit residues: 49.2485 Evaluate side-chains 189 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 185 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 0.0470 chunk 75 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 324 ASN A 363 ASN A 832 GLN A 941 HIS ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6698 Z= 0.223 Angle : 0.744 8.933 9138 Z= 0.383 Chirality : 0.044 0.244 1076 Planarity : 0.004 0.039 1104 Dihedral : 8.518 56.340 1248 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.58 % Favored : 89.93 % Rotamer: Outliers : 0.30 % Allowed : 3.46 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.85 (0.27), residues: 804 helix: -0.44 (0.22), residues: 486 sheet: None (None), residues: 0 loop : -4.37 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 826 HIS 0.007 0.001 HIS A 590 PHE 0.027 0.002 PHE A 852 TYR 0.032 0.002 TYR A1011 ARG 0.002 0.000 ARG A1132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 216 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9361 (tp) cc_final: 0.9061 (tp) REVERT: A 233 ARG cc_start: 0.8982 (mtt180) cc_final: 0.8752 (mtt-85) REVERT: A 383 ARG cc_start: 0.7952 (mtt180) cc_final: 0.6581 (tpt-90) REVERT: A 453 MET cc_start: 0.4687 (pmm) cc_final: 0.4430 (pmm) REVERT: A 464 MET cc_start: 0.8795 (mmm) cc_final: 0.8402 (mmm) REVERT: A 465 MET cc_start: 0.8137 (ttt) cc_final: 0.7904 (tpp) REVERT: A 540 ILE cc_start: 0.9249 (pt) cc_final: 0.9010 (tp) REVERT: A 573 ASP cc_start: 0.8597 (m-30) cc_final: 0.8153 (m-30) REVERT: A 578 CYS cc_start: 0.9290 (m) cc_final: 0.8974 (m) REVERT: A 581 TRP cc_start: 0.8968 (t-100) cc_final: 0.8127 (t-100) REVERT: A 596 THR cc_start: 0.9400 (p) cc_final: 0.9178 (p) REVERT: A 597 VAL cc_start: 0.9718 (p) cc_final: 0.9422 (p) REVERT: A 645 TYR cc_start: 0.9463 (t80) cc_final: 0.9249 (t80) REVERT: A 707 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8236 (tm-30) REVERT: A 725 PHE cc_start: 0.8455 (t80) cc_final: 0.8064 (t80) REVERT: A 765 ASP cc_start: 0.7167 (m-30) cc_final: 0.6952 (m-30) REVERT: A 796 GLU cc_start: 0.9016 (tt0) cc_final: 0.8088 (tm-30) REVERT: A 798 ASN cc_start: 0.7880 (p0) cc_final: 0.7149 (t0) REVERT: A 927 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.9002 (m-10) REVERT: A 950 TRP cc_start: 0.8883 (t-100) cc_final: 0.8523 (t-100) REVERT: A 970 ASN cc_start: 0.8375 (p0) cc_final: 0.8166 (p0) REVERT: A 1033 GLU cc_start: 0.9173 (pm20) cc_final: 0.8960 (pm20) REVERT: A 1043 SER cc_start: 0.9324 (m) cc_final: 0.9064 (t) REVERT: A 1096 MET cc_start: 0.8827 (ttt) cc_final: 0.8559 (ttt) REVERT: A 1112 MET cc_start: 0.8219 (ppp) cc_final: 0.7847 (ppp) REVERT: A 1113 MET cc_start: 0.8593 (ttp) cc_final: 0.7646 (ttp) outliers start: 2 outliers final: 0 residues processed: 218 average time/residue: 0.1398 time to fit residues: 43.0701 Evaluate side-chains 170 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 0.0010 chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 324 ASN A 559 ASN A 832 GLN A 837 GLN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6698 Z= 0.205 Angle : 0.676 8.365 9138 Z= 0.349 Chirality : 0.042 0.181 1076 Planarity : 0.004 0.039 1104 Dihedral : 8.197 59.384 1248 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.20 % Favored : 89.30 % Rotamer: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.29), residues: 804 helix: 0.16 (0.23), residues: 485 sheet: None (None), residues: 0 loop : -4.05 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 826 HIS 0.008 0.001 HIS A 590 PHE 0.025 0.002 PHE A 839 TYR 0.017 0.002 TYR A1011 ARG 0.001 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.9133 (t0) cc_final: 0.8881 (t0) REVERT: A 220 LEU cc_start: 0.8878 (pp) cc_final: 0.8552 (pp) REVERT: A 221 LEU cc_start: 0.9457 (tp) cc_final: 0.9095 (tp) REVERT: A 383 ARG cc_start: 0.8023 (mtt180) cc_final: 0.6711 (tpt-90) REVERT: A 453 MET cc_start: 0.5033 (pmm) cc_final: 0.4700 (pmm) REVERT: A 465 MET cc_start: 0.8285 (ttt) cc_final: 0.7930 (tpp) REVERT: A 530 MET cc_start: 0.9296 (tpp) cc_final: 0.9014 (tpp) REVERT: A 536 ILE cc_start: 0.9188 (mm) cc_final: 0.8893 (mm) REVERT: A 578 CYS cc_start: 0.9354 (m) cc_final: 0.9088 (m) REVERT: A 581 TRP cc_start: 0.8932 (t-100) cc_final: 0.7850 (t-100) REVERT: A 596 THR cc_start: 0.9438 (p) cc_final: 0.9200 (p) REVERT: A 597 VAL cc_start: 0.9700 (p) cc_final: 0.9498 (p) REVERT: A 645 TYR cc_start: 0.9387 (t80) cc_final: 0.9096 (t80) REVERT: A 707 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8233 (tm-30) REVERT: A 725 PHE cc_start: 0.8322 (t80) cc_final: 0.7887 (t80) REVERT: A 765 ASP cc_start: 0.7166 (m-30) cc_final: 0.6789 (m-30) REVERT: A 781 GLU cc_start: 0.8302 (tt0) cc_final: 0.7774 (tp30) REVERT: A 791 TRP cc_start: 0.8488 (m-10) cc_final: 0.8100 (m-10) REVERT: A 798 ASN cc_start: 0.7873 (p0) cc_final: 0.6926 (t0) REVERT: A 970 ASN cc_start: 0.8404 (p0) cc_final: 0.8165 (p0) REVERT: A 972 GLU cc_start: 0.8354 (tt0) cc_final: 0.7987 (tt0) REVERT: A 1083 MET cc_start: 0.9022 (mmm) cc_final: 0.8352 (ttm) REVERT: A 1096 MET cc_start: 0.8869 (ttt) cc_final: 0.8619 (ttt) REVERT: A 1112 MET cc_start: 0.8262 (ppp) cc_final: 0.7950 (ppp) REVERT: A 1113 MET cc_start: 0.8647 (ttp) cc_final: 0.7764 (ttp) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1550 time to fit residues: 44.6922 Evaluate side-chains 171 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 21 optimal weight: 0.0010 chunk 66 optimal weight: 0.7980 overall best weight: 0.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 324 ASN A 356 ASN A 644 ASN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 ASN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6698 Z= 0.174 Angle : 0.657 8.187 9138 Z= 0.338 Chirality : 0.042 0.179 1076 Planarity : 0.004 0.039 1104 Dihedral : 7.853 59.643 1248 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.20 % Favored : 89.43 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.88 (0.30), residues: 804 helix: 0.40 (0.23), residues: 484 sheet: -5.31 (0.54), residues: 16 loop : -3.92 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 826 HIS 0.008 0.001 HIS A 590 PHE 0.028 0.002 PHE A 839 TYR 0.039 0.002 TYR A1011 ARG 0.001 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 218 ASP cc_start: 0.9091 (t0) cc_final: 0.8878 (t0) REVERT: A 220 LEU cc_start: 0.8835 (pp) cc_final: 0.8576 (pp) REVERT: A 221 LEU cc_start: 0.9438 (tp) cc_final: 0.9108 (tp) REVERT: A 383 ARG cc_start: 0.7965 (mtt180) cc_final: 0.6634 (tpt-90) REVERT: A 453 MET cc_start: 0.4516 (pmm) cc_final: 0.4117 (pmm) REVERT: A 465 MET cc_start: 0.8249 (ttt) cc_final: 0.7954 (tmm) REVERT: A 518 MET cc_start: 0.8738 (ttm) cc_final: 0.8419 (tpp) REVERT: A 530 MET cc_start: 0.9289 (tpp) cc_final: 0.7856 (tpp) REVERT: A 536 ILE cc_start: 0.9022 (mm) cc_final: 0.8691 (mm) REVERT: A 557 PHE cc_start: 0.9115 (p90) cc_final: 0.8826 (p90) REVERT: A 578 CYS cc_start: 0.9323 (m) cc_final: 0.9034 (m) REVERT: A 581 TRP cc_start: 0.8889 (t-100) cc_final: 0.8670 (t-100) REVERT: A 645 TYR cc_start: 0.9369 (t80) cc_final: 0.8993 (t80) REVERT: A 651 TRP cc_start: 0.8308 (m100) cc_final: 0.7930 (m100) REVERT: A 725 PHE cc_start: 0.8380 (t80) cc_final: 0.7845 (t80) REVERT: A 765 ASP cc_start: 0.7012 (m-30) cc_final: 0.6729 (m-30) REVERT: A 781 GLU cc_start: 0.8176 (tt0) cc_final: 0.7707 (tp30) REVERT: A 798 ASN cc_start: 0.7753 (p0) cc_final: 0.6832 (t0) REVERT: A 970 ASN cc_start: 0.8345 (p0) cc_final: 0.8106 (p0) REVERT: A 1083 MET cc_start: 0.8993 (mmm) cc_final: 0.8240 (ttm) REVERT: A 1096 MET cc_start: 0.8828 (ttt) cc_final: 0.8621 (ttt) REVERT: A 1112 MET cc_start: 0.8234 (ppp) cc_final: 0.7806 (ppp) REVERT: A 1113 MET cc_start: 0.8652 (ttp) cc_final: 0.7612 (ttp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1335 time to fit residues: 39.1693 Evaluate side-chains 169 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 356 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6698 Z= 0.179 Angle : 0.643 7.299 9138 Z= 0.333 Chirality : 0.041 0.173 1076 Planarity : 0.004 0.040 1104 Dihedral : 7.581 58.683 1248 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.33 % Favored : 90.17 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.77 (0.29), residues: 804 helix: 0.54 (0.23), residues: 487 sheet: -5.06 (0.65), residues: 16 loop : -4.03 (0.30), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 826 HIS 0.006 0.001 HIS A 590 PHE 0.024 0.002 PHE A 839 TYR 0.045 0.002 TYR A1011 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 220 LEU cc_start: 0.8729 (pp) cc_final: 0.8423 (pp) REVERT: A 221 LEU cc_start: 0.9356 (tp) cc_final: 0.8892 (tp) REVERT: A 383 ARG cc_start: 0.8033 (mtt180) cc_final: 0.6722 (tpt-90) REVERT: A 453 MET cc_start: 0.4759 (pmm) cc_final: 0.3850 (pmm) REVERT: A 465 MET cc_start: 0.8390 (ttt) cc_final: 0.7952 (tmm) REVERT: A 518 MET cc_start: 0.8721 (ttm) cc_final: 0.8374 (tpp) REVERT: A 530 MET cc_start: 0.9298 (tpp) cc_final: 0.8105 (tpt) REVERT: A 536 ILE cc_start: 0.8959 (mm) cc_final: 0.8670 (mm) REVERT: A 578 CYS cc_start: 0.9301 (m) cc_final: 0.9067 (m) REVERT: A 581 TRP cc_start: 0.8912 (t-100) cc_final: 0.8711 (t-100) REVERT: A 645 TYR cc_start: 0.9283 (t80) cc_final: 0.8923 (t80) REVERT: A 651 TRP cc_start: 0.8116 (m100) cc_final: 0.7830 (m100) REVERT: A 725 PHE cc_start: 0.8215 (t80) cc_final: 0.7948 (t80) REVERT: A 765 ASP cc_start: 0.7039 (m-30) cc_final: 0.6709 (m-30) REVERT: A 781 GLU cc_start: 0.8218 (tt0) cc_final: 0.7712 (tp30) REVERT: A 791 TRP cc_start: 0.7598 (m-10) cc_final: 0.7259 (m-10) REVERT: A 798 ASN cc_start: 0.7741 (p0) cc_final: 0.7006 (t0) REVERT: A 1096 MET cc_start: 0.8900 (ttt) cc_final: 0.8589 (ttt) REVERT: A 1113 MET cc_start: 0.8602 (ttp) cc_final: 0.7607 (ttp) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1316 time to fit residues: 40.6241 Evaluate side-chains 170 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 47 optimal weight: 0.1980 chunk 19 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6698 Z= 0.231 Angle : 0.693 11.318 9138 Z= 0.359 Chirality : 0.043 0.166 1076 Planarity : 0.004 0.040 1104 Dihedral : 7.773 59.885 1248 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.57 % Favored : 88.93 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: -1.81 (0.29), residues: 804 helix: 0.40 (0.23), residues: 493 sheet: -4.83 (0.77), residues: 12 loop : -3.96 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 826 HIS 0.005 0.001 HIS A 590 PHE 0.019 0.002 PHE A 725 TYR 0.050 0.002 TYR A1011 ARG 0.001 0.000 ARG A1132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9442 (tp) cc_final: 0.9191 (tp) REVERT: A 383 ARG cc_start: 0.8037 (mtt180) cc_final: 0.6703 (tpt-90) REVERT: A 421 TYR cc_start: 0.8571 (t80) cc_final: 0.8360 (t80) REVERT: A 453 MET cc_start: 0.5112 (pmm) cc_final: 0.4551 (pmm) REVERT: A 465 MET cc_start: 0.8406 (ttt) cc_final: 0.7937 (tmm) REVERT: A 518 MET cc_start: 0.8858 (ttm) cc_final: 0.8343 (tpp) REVERT: A 530 MET cc_start: 0.9294 (tpp) cc_final: 0.8161 (tpt) REVERT: A 536 ILE cc_start: 0.9072 (mm) cc_final: 0.8771 (mm) REVERT: A 578 CYS cc_start: 0.9397 (m) cc_final: 0.9121 (m) REVERT: A 581 TRP cc_start: 0.8989 (t-100) cc_final: 0.8776 (t-100) REVERT: A 651 TRP cc_start: 0.8300 (m100) cc_final: 0.8081 (m100) REVERT: A 713 ILE cc_start: 0.9060 (mm) cc_final: 0.8856 (mm) REVERT: A 725 PHE cc_start: 0.8338 (t80) cc_final: 0.7914 (t80) REVERT: A 765 ASP cc_start: 0.6999 (m-30) cc_final: 0.6662 (m-30) REVERT: A 781 GLU cc_start: 0.8272 (tt0) cc_final: 0.7822 (tp30) REVERT: A 791 TRP cc_start: 0.7916 (m-10) cc_final: 0.7462 (m-10) REVERT: A 798 ASN cc_start: 0.7844 (p0) cc_final: 0.6939 (t0) REVERT: A 856 PHE cc_start: 0.8764 (m-80) cc_final: 0.8529 (m-80) REVERT: A 895 MET cc_start: -0.0410 (mmt) cc_final: -0.1373 (mtp) REVERT: A 950 TRP cc_start: 0.9015 (t-100) cc_final: 0.8807 (t-100) REVERT: A 1096 MET cc_start: 0.8900 (ttt) cc_final: 0.8618 (ttt) REVERT: A 1112 MET cc_start: 0.8101 (ppp) cc_final: 0.7773 (ppp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1336 time to fit residues: 41.0392 Evaluate side-chains 168 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 GLN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6698 Z= 0.186 Angle : 0.661 6.867 9138 Z= 0.341 Chirality : 0.042 0.183 1076 Planarity : 0.004 0.040 1104 Dihedral : 7.499 59.444 1248 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.33 % Favored : 90.17 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.66 (0.29), residues: 804 helix: 0.54 (0.24), residues: 485 sheet: -4.35 (1.04), residues: 12 loop : -3.84 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 826 HIS 0.006 0.001 HIS A 590 PHE 0.019 0.002 PHE A1111 TYR 0.035 0.002 TYR A1011 ARG 0.002 0.000 ARG A 302 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 0.740 Fit side-chains REVERT: A 220 LEU cc_start: 0.8737 (pp) cc_final: 0.8520 (pp) REVERT: A 221 LEU cc_start: 0.9374 (tp) cc_final: 0.9126 (tp) REVERT: A 383 ARG cc_start: 0.7979 (mtt180) cc_final: 0.6721 (tpt170) REVERT: A 465 MET cc_start: 0.8678 (ttt) cc_final: 0.7699 (tmm) REVERT: A 518 MET cc_start: 0.8897 (ttm) cc_final: 0.8415 (tpp) REVERT: A 530 MET cc_start: 0.9297 (tpp) cc_final: 0.8026 (tpt) REVERT: A 536 ILE cc_start: 0.8968 (mm) cc_final: 0.8655 (mm) REVERT: A 558 MET cc_start: 0.9265 (mpp) cc_final: 0.8905 (mpp) REVERT: A 651 TRP cc_start: 0.8244 (m100) cc_final: 0.7877 (m100) REVERT: A 725 PHE cc_start: 0.8448 (t80) cc_final: 0.7802 (t80) REVERT: A 765 ASP cc_start: 0.6995 (m-30) cc_final: 0.6662 (m-30) REVERT: A 781 GLU cc_start: 0.8269 (tt0) cc_final: 0.7706 (tm-30) REVERT: A 791 TRP cc_start: 0.7757 (m-10) cc_final: 0.7445 (m-10) REVERT: A 798 ASN cc_start: 0.7851 (p0) cc_final: 0.6940 (t0) REVERT: A 972 GLU cc_start: 0.8211 (tt0) cc_final: 0.7939 (tt0) REVERT: A 1007 ILE cc_start: 0.8221 (tt) cc_final: 0.7770 (tp) REVERT: A 1096 MET cc_start: 0.8880 (ttt) cc_final: 0.8585 (ttt) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1380 time to fit residues: 39.7920 Evaluate side-chains 158 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6698 Z= 0.179 Angle : 0.661 7.539 9138 Z= 0.338 Chirality : 0.042 0.175 1076 Planarity : 0.004 0.041 1104 Dihedral : 7.359 56.574 1248 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.95 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.70 (0.29), residues: 804 helix: 0.46 (0.23), residues: 489 sheet: -4.27 (1.13), residues: 14 loop : -3.83 (0.30), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 950 HIS 0.009 0.001 HIS A 377 PHE 0.025 0.002 PHE A 839 TYR 0.032 0.002 TYR A1011 ARG 0.004 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 220 LEU cc_start: 0.8826 (pp) cc_final: 0.8492 (pp) REVERT: A 383 ARG cc_start: 0.7998 (mtt180) cc_final: 0.6742 (tpt170) REVERT: A 465 MET cc_start: 0.8595 (ttt) cc_final: 0.7752 (tmm) REVERT: A 518 MET cc_start: 0.8923 (ttm) cc_final: 0.8358 (tpp) REVERT: A 530 MET cc_start: 0.9258 (tpp) cc_final: 0.8141 (tpp) REVERT: A 725 PHE cc_start: 0.8513 (t80) cc_final: 0.8035 (t80) REVERT: A 765 ASP cc_start: 0.6991 (m-30) cc_final: 0.6601 (m-30) REVERT: A 781 GLU cc_start: 0.8294 (tt0) cc_final: 0.7728 (tm-30) REVERT: A 791 TRP cc_start: 0.7720 (m-10) cc_final: 0.7364 (m-10) REVERT: A 796 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8179 (tm-30) REVERT: A 798 ASN cc_start: 0.7858 (p0) cc_final: 0.7211 (t0) REVERT: A 972 GLU cc_start: 0.8189 (tt0) cc_final: 0.7936 (tt0) REVERT: A 1007 ILE cc_start: 0.8208 (tt) cc_final: 0.7682 (tp) REVERT: A 1096 MET cc_start: 0.8886 (ttt) cc_final: 0.8587 (ttt) REVERT: A 1113 MET cc_start: 0.8597 (ttp) cc_final: 0.7758 (ttp) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1356 time to fit residues: 38.5705 Evaluate side-chains 155 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 chunk 32 optimal weight: 0.2980 chunk 58 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 0.0170 chunk 37 optimal weight: 0.7980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6698 Z= 0.171 Angle : 0.667 7.873 9138 Z= 0.341 Chirality : 0.043 0.213 1076 Planarity : 0.004 0.041 1104 Dihedral : 7.165 54.379 1248 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.83 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.68 (0.29), residues: 804 helix: 0.49 (0.23), residues: 487 sheet: -3.95 (1.38), residues: 14 loop : -3.82 (0.30), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 651 HIS 0.008 0.001 HIS A 659 PHE 0.034 0.002 PHE A 554 TYR 0.031 0.002 TYR A 645 ARG 0.002 0.000 ARG A 302 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 302 ARG cc_start: 0.7668 (ptp90) cc_final: 0.6043 (ptp90) REVERT: A 383 ARG cc_start: 0.7999 (mtt180) cc_final: 0.6767 (tpt170) REVERT: A 421 TYR cc_start: 0.8652 (t80) cc_final: 0.8451 (t80) REVERT: A 453 MET cc_start: 0.4639 (pmm) cc_final: 0.3358 (pmm) REVERT: A 465 MET cc_start: 0.8621 (ttt) cc_final: 0.7821 (tmm) REVERT: A 518 MET cc_start: 0.8838 (ttm) cc_final: 0.8355 (tpp) REVERT: A 584 THR cc_start: 0.9616 (p) cc_final: 0.9305 (p) REVERT: A 587 ASP cc_start: 0.8738 (p0) cc_final: 0.8478 (m-30) REVERT: A 645 TYR cc_start: 0.9286 (t80) cc_final: 0.8906 (t80) REVERT: A 725 PHE cc_start: 0.8417 (t80) cc_final: 0.7979 (t80) REVERT: A 765 ASP cc_start: 0.6979 (m-30) cc_final: 0.6568 (m-30) REVERT: A 781 GLU cc_start: 0.8274 (tt0) cc_final: 0.7719 (tm-30) REVERT: A 791 TRP cc_start: 0.7587 (m-10) cc_final: 0.7279 (m-10) REVERT: A 796 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8154 (tm-30) REVERT: A 798 ASN cc_start: 0.7799 (p0) cc_final: 0.7180 (t0) REVERT: A 810 LEU cc_start: 0.8927 (pt) cc_final: 0.8566 (pp) REVERT: A 972 GLU cc_start: 0.8222 (tt0) cc_final: 0.7981 (tt0) REVERT: A 1007 ILE cc_start: 0.8056 (tt) cc_final: 0.7549 (tp) REVERT: A 1096 MET cc_start: 0.8885 (ttt) cc_final: 0.8636 (ttt) REVERT: A 1113 MET cc_start: 0.8524 (ttp) cc_final: 0.7741 (ttp) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1377 time to fit residues: 38.7661 Evaluate side-chains 155 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.0000 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 0.0020 chunk 50 optimal weight: 0.0030 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 HIS ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.5758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6698 Z= 0.170 Angle : 0.663 8.660 9138 Z= 0.337 Chirality : 0.042 0.223 1076 Planarity : 0.004 0.041 1104 Dihedral : 6.964 51.717 1248 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.07 % Favored : 89.43 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.62 (0.29), residues: 804 helix: 0.53 (0.24), residues: 482 sheet: -3.89 (1.43), residues: 14 loop : -3.73 (0.30), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 651 HIS 0.006 0.001 HIS A 590 PHE 0.027 0.002 PHE A 554 TYR 0.024 0.002 TYR A1011 ARG 0.002 0.000 ARG A 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8184 (mm-30) REVERT: A 383 ARG cc_start: 0.8018 (mtt180) cc_final: 0.6785 (tpt170) REVERT: A 453 MET cc_start: 0.4037 (pmm) cc_final: 0.3704 (pmm) REVERT: A 465 MET cc_start: 0.8511 (ttt) cc_final: 0.7859 (tmm) REVERT: A 557 PHE cc_start: 0.9194 (p90) cc_final: 0.8972 (p90) REVERT: A 584 THR cc_start: 0.9628 (p) cc_final: 0.9305 (p) REVERT: A 587 ASP cc_start: 0.8691 (p0) cc_final: 0.8461 (m-30) REVERT: A 765 ASP cc_start: 0.6802 (m-30) cc_final: 0.6440 (m-30) REVERT: A 781 GLU cc_start: 0.8263 (tt0) cc_final: 0.7703 (tm-30) REVERT: A 789 VAL cc_start: 0.8829 (m) cc_final: 0.8610 (m) REVERT: A 791 TRP cc_start: 0.7521 (m-10) cc_final: 0.7169 (m-10) REVERT: A 796 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8130 (tm-30) REVERT: A 798 ASN cc_start: 0.7784 (p0) cc_final: 0.7217 (t0) REVERT: A 810 LEU cc_start: 0.8919 (pt) cc_final: 0.8555 (pp) REVERT: A 972 GLU cc_start: 0.8197 (tt0) cc_final: 0.7290 (tt0) REVERT: A 1007 ILE cc_start: 0.7999 (tt) cc_final: 0.7468 (tp) REVERT: A 1096 MET cc_start: 0.8823 (ttt) cc_final: 0.8591 (ttt) REVERT: A 1113 MET cc_start: 0.8485 (ttp) cc_final: 0.7697 (ttp) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1336 time to fit residues: 38.3098 Evaluate side-chains 154 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.0770 chunk 18 optimal weight: 0.0040 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 47 optimal weight: 0.0670 chunk 75 optimal weight: 0.7980 overall best weight: 0.3488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 324 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.150818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127798 restraints weight = 13392.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131512 restraints weight = 8393.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.134160 restraints weight = 5795.579| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6698 Z= 0.170 Angle : 0.672 8.552 9138 Z= 0.341 Chirality : 0.043 0.221 1076 Planarity : 0.004 0.041 1104 Dihedral : 7.006 51.011 1248 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.20 % Favored : 90.30 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.60 (0.29), residues: 804 helix: 0.53 (0.23), residues: 484 sheet: -3.32 (1.58), residues: 12 loop : -3.74 (0.29), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 950 HIS 0.006 0.001 HIS A 590 PHE 0.026 0.002 PHE A 554 TYR 0.025 0.002 TYR A 645 ARG 0.002 0.000 ARG A 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1700.02 seconds wall clock time: 32 minutes 29.70 seconds (1949.70 seconds total)