Starting phenix.real_space_refine on Fri Dec 8 01:41:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe6_22144/12_2023/6xe6_22144.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe6_22144/12_2023/6xe6_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_2023/6xe6_22144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe6_22144/12_2023/6xe6_22144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe6_22144/12_2023/6xe6_22144.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe6_22144/12_2023/6xe6_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-1.21rc1-5172/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: 4.28, 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: 2.71 Conformation dependent library (CDL) restraints added in 1.2 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: 0.51 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: 1.58 Time building geometry restraints manager: 2.96 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: 3.140 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: 4.180 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 21.460 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.000 ------------------------------------------------------------------------------- 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 : 0.750 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 236 average time/residue: 0.1534 time to fit residues: 49.7955 Evaluate side-chains 184 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0809 time to fit residues: 1.3192 ------------------------------------------------------------------------------- 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: 0.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 0.0980 chunk 75 optimal weight: 0.6980 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 239 ASN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6698 Z= 0.234 Angle : 0.740 8.026 9138 Z= 0.383 Chirality : 0.044 0.199 1076 Planarity : 0.004 0.038 1104 Dihedral : 8.629 56.163 1248 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.70 % Favored : 89.68 % Rotamer: Outliers : 0.15 % Allowed : 3.76 % 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: -2.87 (0.27), residues: 804 helix: -0.46 (0.22), residues: 485 sheet: None (None), residues: 0 loop : -4.37 (0.28), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 826 HIS 0.008 0.001 HIS A 590 PHE 0.031 0.002 PHE A 725 TYR 0.014 0.002 TYR A1056 ARG 0.002 0.000 ARG A 383 *********************** 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 212 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.1373 time to fit residues: 41.3806 Evaluate side-chains 164 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.760 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0024 ------------------------------------------------------------------------------- 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: 7.9990 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 778 HIS A 832 GLN A 837 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6698 Z= 0.233 Angle : 0.702 8.165 9138 Z= 0.365 Chirality : 0.044 0.179 1076 Planarity : 0.004 0.039 1104 Dihedral : 8.368 58.601 1248 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.82 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % 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: -2.21 (0.29), residues: 804 helix: 0.11 (0.23), residues: 483 sheet: None (None), residues: 0 loop : -4.15 (0.29), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 826 HIS 0.007 0.001 HIS A 590 PHE 0.028 0.002 PHE A 839 TYR 0.013 0.002 TYR A 768 ARG 0.001 0.000 ARG A1132 *********************** 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 : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1411 time to fit residues: 40.3390 Evaluate side-chains 170 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5203 ------------------------------------------------------------------------------- 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: 0.9980 chunk 56 optimal weight: 0.0270 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 0.0060 chunk 75 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.5054 ------------------------------------------------------------------------------- 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 644 ASN A 964 ASN ** A1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6698 Z= 0.190 Angle : 0.677 7.368 9138 Z= 0.347 Chirality : 0.042 0.178 1076 Planarity : 0.004 0.039 1104 Dihedral : 7.966 55.478 1248 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.45 % Favored : 90.17 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % 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: -1.89 (0.29), residues: 804 helix: 0.36 (0.23), residues: 482 sheet: None (None), residues: 0 loop : -3.99 (0.30), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 791 HIS 0.008 0.001 HIS A 590 PHE 0.027 0.002 PHE A 839 TYR 0.019 0.001 TYR A 636 ARG 0.001 0.000 ARG A 383 *********************** 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 199 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1694 time to fit residues: 48.9767 Evaluate side-chains 167 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0416 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 356 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6698 Z= 0.188 Angle : 0.661 7.100 9138 Z= 0.339 Chirality : 0.041 0.175 1076 Planarity : 0.004 0.040 1104 Dihedral : 7.746 59.129 1248 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.70 % Favored : 89.68 % 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: -1.76 (0.29), residues: 804 helix: 0.53 (0.23), residues: 482 sheet: -4.86 (0.68), residues: 16 loop : -3.95 (0.30), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 826 HIS 0.006 0.001 HIS A 590 PHE 0.031 0.002 PHE A 725 TYR 0.025 0.002 TYR A1011 ARG 0.002 0.000 ARG A 383 *********************** 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 197 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1295 time to fit residues: 36.9572 Evaluate side-chains 167 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.722 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9149 ------------------------------------------------------------------------------- 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: 0.9980 chunk 15 optimal weight: 0.0570 chunk 47 optimal weight: 0.0060 chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 overall best weight: 0.4914 ------------------------------------------------------------------------------- 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 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.5007 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= 0.180 Angle : 0.658 7.541 9138 Z= 0.339 Chirality : 0.042 0.178 1076 Planarity : 0.004 0.042 1104 Dihedral : 7.490 54.698 1248 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.45 % Favored : 90.05 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: 0.56 (0.23), residues: 479 sheet: -4.83 (0.69), residues: 16 loop : -3.80 (0.30), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 826 HIS 0.006 0.001 HIS A 590 PHE 0.039 0.002 PHE A 725 TYR 0.047 0.002 TYR A1011 ARG 0.001 0.000 ARG A 302 *********************** 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 203 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1465 time to fit residues: 42.9654 Evaluate side-chains 164 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0347 ------------------------------------------------------------------------------- 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: 5.9990 chunk 45 optimal weight: 0.2980 chunk 58 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7489 moved from start: 0.5337 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 : 0.678 10.281 9138 Z= 0.343 Chirality : 0.041 0.179 1076 Planarity : 0.004 0.045 1104 Dihedral : 7.233 59.279 1248 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.20 % Favored : 90.30 % 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: -1.55 (0.29), residues: 804 helix: 0.62 (0.24), residues: 481 sheet: -4.01 (1.22), residues: 10 loop : -3.76 (0.30), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 651 HIS 0.006 0.001 HIS A 590 PHE 0.032 0.002 PHE A 839 TYR 0.035 0.002 TYR A1011 ARG 0.001 0.000 ARG A 383 *********************** 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 202 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1445 time to fit residues: 41.1161 Evaluate side-chains 164 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.663 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9868 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 54 optimal weight: 0.0000 chunk 39 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN 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** ** 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: 0.7553 moved from start: 0.5312 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= 0.205 Angle : 0.692 12.032 9138 Z= 0.349 Chirality : 0.042 0.197 1076 Planarity : 0.004 0.046 1104 Dihedral : 7.447 56.080 1248 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.44 % Favored : 88.06 % Rotamer: Outliers : 0.15 % Allowed : 1.20 % Favored : 98.65 % 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: -1.60 (0.29), residues: 804 helix: 0.51 (0.23), residues: 489 sheet: -4.27 (1.20), residues: 12 loop : -3.74 (0.31), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 651 HIS 0.004 0.001 HIS A 590 PHE 0.027 0.002 PHE A 839 TYR 0.031 0.002 TYR A1011 ARG 0.005 0.000 ARG A 302 *********************** 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 195 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 195 average time/residue: 0.1382 time to fit residues: 38.8242 Evaluate side-chains 155 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.725 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9960 ------------------------------------------------------------------------------- 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: 3.9990 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 0.0980 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5557 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= 0.180 Angle : 0.680 8.432 9138 Z= 0.345 Chirality : 0.042 0.221 1076 Planarity : 0.004 0.044 1104 Dihedral : 7.413 58.813 1248 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.70 % Favored : 89.80 % 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: -1.54 (0.29), residues: 804 helix: 0.56 (0.23), residues: 488 sheet: -3.92 (1.20), residues: 14 loop : -3.69 (0.31), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 237 HIS 0.005 0.001 HIS A 590 PHE 0.039 0.002 PHE A1126 TYR 0.028 0.001 TYR A1011 ARG 0.003 0.000 ARG A 763 *********************** 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 194 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1454 time to fit residues: 40.6501 Evaluate side-chains 156 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.747 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9866 ------------------------------------------------------------------------------- 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: 0.9980 chunk 82 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 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: 0.7502 moved from start: 0.5648 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= 0.188 Angle : 0.702 9.637 9138 Z= 0.355 Chirality : 0.043 0.209 1076 Planarity : 0.004 0.043 1104 Dihedral : 7.370 58.800 1248 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.70 % Favored : 88.81 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -1.56 (0.29), residues: 804 helix: 0.53 (0.23), residues: 483 sheet: -3.44 (1.30), residues: 14 loop : -3.64 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 826 HIS 0.008 0.001 HIS A 659 PHE 0.033 0.002 PHE A1126 TYR 0.027 0.002 TYR A1011 ARG 0.001 0.000 ARG A 913 ********************** 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 195 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1361 time to fit residues: 38.1412 Evaluate side-chains 158 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.743 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0281 ------------------------------------------------------------------------------- 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: 0.5980 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 0.0470 chunk 47 optimal weight: 0.0970 chunk 75 optimal weight: 0.6980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 239 ASN A 324 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.148741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126089 restraints weight = 13691.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.129826 restraints weight = 8599.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132493 restraints weight = 5913.294| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6698 Z= 0.177 Angle : 0.695 9.647 9138 Z= 0.352 Chirality : 0.042 0.218 1076 Planarity : 0.004 0.044 1104 Dihedral : 7.246 59.922 1248 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.83 % Favored : 89.68 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -1.57 (0.29), residues: 804 helix: 0.49 (0.23), residues: 482 sheet: -2.96 (1.46), residues: 14 loop : -3.60 (0.30), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 826 HIS 0.005 0.001 HIS A 590 PHE 0.028 0.002 PHE A1126 TYR 0.023 0.002 TYR A1011 ARG 0.001 0.000 ARG A 913 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1720.69 seconds wall clock time: 32 minutes 30.29 seconds (1950.29 seconds total)