Starting phenix.real_space_refine (version: dev) on Sun Dec 11 18:30:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe6_22144/12_2022/6xe6_22144_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe6_22144/12_2022/6xe6_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_22144/12_2022/6xe6_22144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe6_22144/12_2022/6xe6_22144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe6_22144/12_2022/6xe6_22144_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe6_22144/12_2022/6xe6_22144_updated.pdb" } resolution = 4.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Convert atoms to be neutral 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-4807/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: 4.31, per 1000 atoms: 0.66 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: 2.68 Conformation dependent library (CDL) restraints added in 1.1 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... running ksdssp... Secondary structure from input PDB file: 26 helices and 0 sheets defined 57.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 189 through 209 Processing helix chain 'A' and resid 229 through 242 removed outlier: 3.527A pdb=" N LEU A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 236 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 238 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A 240 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 355 through 358 No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 371 through 384 Processing helix chain 'A' and resid 424 through 431 removed outlier: 3.698A pdb=" N LEU A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 492 through 522 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 Processing helix chain 'A' and resid 525 through 548 Processing helix chain 'A' and resid 558 through 569 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 572 through 587 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 593 through 624 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) removed outlier: 4.621A pdb=" N VAL A 624 " --> pdb=" O TYR A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 660 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 720 through 736 Processing helix chain 'A' and resid 760 through 768 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 824 through 836 Processing helix chain 'A' and resid 853 through 861 Processing helix chain 'A' and resid 885 through 895 Processing helix chain 'A' and resid 938 through 956 removed outlier: 3.515A pdb=" N PHE A 943 " --> pdb=" O MET A 940 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 945 " --> pdb=" O GLN A 942 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A 948 " --> pdb=" O LYS A 945 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 949 " --> pdb=" O GLU A 946 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 952 " --> pdb=" O SER A 949 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 955 " --> pdb=" O SER A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 1002 Processing helix chain 'A' and resid 1007 through 1029 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) Processing helix chain 'A' and resid 1037 through 1061 removed outlier: 3.607A pdb=" N THR A1041 " --> pdb=" O GLU A1038 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A1043 " --> pdb=" O VAL A1040 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A1048 " --> pdb=" O ALA A1045 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A1049 " --> pdb=" O VAL A1046 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A1050 " --> pdb=" O GLY A1047 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A1051 " --> pdb=" O LEU A1048 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A1052 " --> pdb=" O SER A1049 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A1054 " --> pdb=" O ASP A1051 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A1058 " --> pdb=" O HIS A1055 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A1059 " --> pdb=" O TYR A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1097 removed outlier: 4.625A pdb=" N MET A1085 " --> pdb=" O SER A1081 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N MET A1097 " --> pdb=" O ALA A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1133 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) 319 hydrogen bonds defined for protein. 870 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: 1.53 Time building geometry restraints manager: 2.76 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=" C1 NAG A1306 " pdb=" O1 NAG A1306 " ideal model delta sigma weight residual 1.390 1.443 -0.053 1.00e-02 1.00e+04 2.77e+01 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 ... (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: 3438 17.13 - 34.26: 321 34.26 - 51.40: 95 51.40 - 68.53: 12 68.53 - 85.66: 2 Dihedral angle restraints: 3868 sinusoidal: 1445 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 3865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 852 0.078 - 0.157: 180 0.157 - 0.235: 32 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: 44 2.62 - 3.38: 9073 3.38 - 4.14: 14509 4.14 - 4.90: 24938 Nonbonded interactions: 48567 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 48562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 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. 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: 0.610 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: 4.270 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.060 Process input model: 20.640 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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= 0.696 Angle : 1.398 10.649 9138 Z= 0.914 Chirality : 0.072 0.392 1076 Planarity : 0.005 0.065 1104 Dihedral : 14.921 85.659 2289 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 % 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 *********************** 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 : 0.680 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 236 average time/residue: 0.1509 time to fit residues: 49.0353 Evaluate side-chains 184 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 0.791 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0950 time to fit residues: 1.4379 ------------------------------------------------------------------------------- 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: 0.7980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 363 ASN ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 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: 0.7600 moved from start: 0.2985 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= 0.225 Angle : 0.722 7.826 9138 Z= 0.373 Chirality : 0.043 0.183 1076 Planarity : 0.004 0.040 1104 Dihedral : 7.996 57.633 940 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.95 % Favored : 89.55 % Rotamer Outliers : 0.30 % 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: -3.14 (0.27), residues: 804 helix: -0.74 (0.22), residues: 483 sheet: None (None), residues: 0 loop : -4.35 (0.28), residues: 321 *********************** 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 210 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 208 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.1356 time to fit residues: 40.6647 Evaluate side-chains 165 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0182 ------------------------------------------------------------------------------- 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: 0.0770 chunk 23 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 6698 Z= 0.188 Angle : 0.670 7.759 9138 Z= 0.343 Chirality : 0.041 0.177 1076 Planarity : 0.004 0.039 1104 Dihedral : 7.789 58.853 940 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.07 % Favored : 89.43 % Rotamer Outliers : 0.15 % 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: -2.53 (0.28), residues: 804 helix: -0.22 (0.23), residues: 485 sheet: None (None), residues: 0 loop : -4.17 (0.29), residues: 319 *********************** 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 203 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.1341 time to fit residues: 39.4239 Evaluate side-chains 169 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.688 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0107 ------------------------------------------------------------------------------- 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: 9.9990 chunk 56 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 0.0670 chunk 36 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 559 ASN A 837 GLN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 ASN A1055 HIS ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 6698 Z= 0.181 Angle : 0.665 8.063 9138 Z= 0.340 Chirality : 0.041 0.172 1076 Planarity : 0.004 0.041 1104 Dihedral : 7.690 59.809 940 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.83 % Favored : 89.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.30 (0.28), residues: 804 helix: -0.04 (0.23), residues: 483 sheet: None (None), residues: 0 loop : -4.04 (0.29), residues: 321 *********************** 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 202 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1299 time to fit residues: 37.7914 Evaluate side-chains 165 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.738 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0085 ------------------------------------------------------------------------------- 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: 6.9990 chunk 1 optimal weight: 6.9990 chunk 59 optimal weight: 0.0470 chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- 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 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 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: 0.7574 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 6698 Z= 0.198 Angle : 0.667 8.009 9138 Z= 0.344 Chirality : 0.041 0.193 1076 Planarity : 0.004 0.041 1104 Dihedral : 7.581 57.266 940 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.07 % Favored : 89.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.15 (0.29), residues: 804 helix: 0.15 (0.23), residues: 475 sheet: -4.60 (0.88), residues: 16 loop : -3.90 (0.30), residues: 313 *********************** 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 213 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 0.723 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1362 time to fit residues: 41.3306 Evaluate side-chains 167 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7724 ------------------------------------------------------------------------------- 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: 0.9990 chunk 15 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 HIS ** 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: 0.7577 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6698 Z= 0.206 Angle : 0.685 7.260 9138 Z= 0.353 Chirality : 0.042 0.164 1076 Planarity : 0.004 0.041 1104 Dihedral : 7.691 59.165 940 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.07 % Favored : 89.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.28), residues: 804 helix: 0.02 (0.23), residues: 478 sheet: -4.39 (0.94), residues: 16 loop : -3.79 (0.30), residues: 310 *********************** 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 201 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1399 time to fit residues: 40.0548 Evaluate side-chains 164 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.692 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0060 ------------------------------------------------------------------------------- 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: 3.9990 chunk 45 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 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 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 HIS ** 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: 0.7527 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6698 Z= 0.184 Angle : 0.690 8.281 9138 Z= 0.349 Chirality : 0.041 0.184 1076 Planarity : 0.004 0.042 1104 Dihedral : 7.582 57.830 940 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.45 % Favored : 89.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.18 (0.29), residues: 804 helix: 0.02 (0.23), residues: 476 sheet: -4.23 (1.02), residues: 18 loop : -3.73 (0.31), residues: 310 *********************** 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 203 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 0.742 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1380 time to fit residues: 39.7317 Evaluate side-chains 162 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0232 ------------------------------------------------------------------------------- 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: 9.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.0570 chunk 50 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 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: 0.7502 moved from start: 0.5327 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= 0.181 Angle : 0.683 8.005 9138 Z= 0.346 Chirality : 0.041 0.181 1076 Planarity : 0.004 0.042 1104 Dihedral : 7.419 58.516 940 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.83 % Favored : 89.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.02 (0.29), residues: 804 helix: 0.13 (0.23), residues: 471 sheet: -3.96 (1.09), residues: 18 loop : -3.60 (0.31), residues: 315 *********************** 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 206 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1397 time to fit residues: 41.0558 Evaluate side-chains 163 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0086 ------------------------------------------------------------------------------- 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: 9.9990 chunk 76 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 0.0970 chunk 78 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 622 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 HIS ** 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: 0.7449 moved from start: 0.5659 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= 0.171 Angle : 0.692 12.447 9138 Z= 0.347 Chirality : 0.042 0.185 1076 Planarity : 0.004 0.042 1104 Dihedral : 7.271 58.518 940 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.83 % Favored : 89.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.91 (0.29), residues: 804 helix: 0.19 (0.23), residues: 472 sheet: -3.85 (1.28), residues: 14 loop : -3.54 (0.31), residues: 318 *********************** 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 202 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1398 time to fit residues: 40.4602 Evaluate side-chains 168 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0321 ------------------------------------------------------------------------------- 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: 0.0980 chunk 82 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 GLN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 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: 0.7446 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6698 Z= 0.175 Angle : 0.682 10.401 9138 Z= 0.344 Chirality : 0.042 0.186 1076 Planarity : 0.004 0.042 1104 Dihedral : 7.121 55.514 940 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.70 % Favored : 89.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.92 (0.29), residues: 804 helix: 0.20 (0.23), residues: 465 sheet: -3.04 (1.94), residues: 10 loop : -3.54 (0.30), residues: 329 ********************** 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 202 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1348 time to fit residues: 39.5413 Evaluate side-chains 167 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.769 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9682 ------------------------------------------------------------------------------- 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: 7.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 3 optimal weight: 0.0040 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 622 ASN A 659 HIS ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122534 restraints weight = 13814.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125883 restraints weight = 8953.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.128289 restraints weight = 6353.476| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6698 Z= 0.175 Angle : 0.684 8.417 9138 Z= 0.346 Chirality : 0.042 0.208 1076 Planarity : 0.004 0.046 1104 Dihedral : 7.028 57.134 940 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.70 % Favored : 89.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.86 (0.29), residues: 804 helix: 0.22 (0.23), residues: 479 sheet: -2.51 (2.06), residues: 10 loop : -3.65 (0.30), residues: 315 =============================================================================== Job complete usr+sys time: 1547.24 seconds wall clock time: 28 minutes 48.15 seconds (1728.15 seconds total)