Starting phenix.real_space_refine on Wed Feb 12 22:11:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xmt_22263/02_2025/6xmt_22263.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xmt_22263/02_2025/6xmt_22263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xmt_22263/02_2025/6xmt_22263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xmt_22263/02_2025/6xmt_22263.map" model { file = "/net/cci-nas-00/data/ceres_data/6xmt_22263/02_2025/6xmt_22263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xmt_22263/02_2025/6xmt_22263.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.057 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 38 5.16 5 Be 1 3.05 5 C 5370 2.51 5 N 1374 2.21 5 O 1537 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8324 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8319 Classifications: {'peptide': 1092} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 49, 'TRANS': 1042} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 164 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.18, per 1000 atoms: 0.62 Number of scatterers: 8324 At special positions: 0 Unit cell: (91.63, 88.06, 145.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 38 16.00 Mg 1 11.99 F 3 9.00 O 1537 8.00 N 1374 7.00 C 5370 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.0 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 46.5% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 28 through 44 removed outlier: 3.804A pdb=" N PHE A 32 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 57 through 74 removed outlier: 3.540A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 156 through 162 removed outlier: 3.866A pdb=" N PHE A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 199 through 214 Processing helix chain 'A' and resid 218 through 247 removed outlier: 3.697A pdb=" N MET A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 336 removed outlier: 4.409A pdb=" N ILE A 336 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.703A pdb=" N GLU A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 388 Processing helix chain 'A' and resid 396 through 425 Processing helix chain 'A' and resid 427 through 441 removed outlier: 3.627A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 463 Processing helix chain 'A' and resid 471 through 480 removed outlier: 3.686A pdb=" N ILE A 475 " --> pdb=" O PRO A 472 " (cutoff:3.500A) Proline residue: A 476 - end of helix removed outlier: 3.507A pdb=" N GLY A 479 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 480 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 removed outlier: 3.791A pdb=" N GLY A 530 " --> pdb=" O ILE A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 606 through 612 removed outlier: 3.777A pdb=" N GLU A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 655 through 660 removed outlier: 4.318A pdb=" N VAL A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 688 Processing helix chain 'A' and resid 700 through 712 Processing helix chain 'A' and resid 753 through 758 Processing helix chain 'A' and resid 766 through 772 Processing helix chain 'A' and resid 778 through 784 Processing helix chain 'A' and resid 795 through 808 removed outlier: 3.940A pdb=" N PHE A 799 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 827 Processing helix chain 'A' and resid 837 through 854 Processing helix chain 'A' and resid 972 through 1010 removed outlier: 3.667A pdb=" N CYS A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1035 Processing helix chain 'A' and resid 1055 through 1084 Processing helix chain 'A' and resid 1099 through 1119 removed outlier: 3.903A pdb=" N THR A1103 " --> pdb=" O SER A1099 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A1108 " --> pdb=" O GLY A1104 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A1117 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1152 removed outlier: 3.742A pdb=" N THR A1152 " --> pdb=" O LEU A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1162 Processing helix chain 'A' and resid 1169 through 1197 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.726A pdb=" N TYR A 102 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER A 15 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 100 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LEU A 17 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N HIS A 98 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 111 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 130 removed outlier: 3.586A pdb=" N PHE A 128 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 267 removed outlier: 4.862A pdb=" N ASN A 257 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 279 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU A 277 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP A 292 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 316 removed outlier: 6.850A pdb=" N SER A 299 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL A 348 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 301 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 344 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 467 through 469 removed outlier: 6.480A pdb=" N GLY A 830 " --> pdb=" O PHE A 964 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N SER A 966 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA A 832 " --> pdb=" O SER A 966 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU A 833 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY A 815 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N CYS A 814 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N CYS A 485 " --> pdb=" O CYS A 814 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N CYS A 484 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE A 696 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N PHE A 486 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER A 693 " --> pdb=" O TRP A 787 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N TYR A 789 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N MET A 695 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE A 763 " --> pdb=" O THR A 786 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL A 788 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 719 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 722 " --> pdb=" O LEU A 733 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 498 through 501 removed outlier: 3.662A pdb=" N VAL A 498 " --> pdb=" O HIS A 672 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE A 670 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 671 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 536 through 537 removed outlier: 3.595A pdb=" N VAL A 536 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 559 through 560 removed outlier: 3.613A pdb=" N ALA A 559 " --> pdb=" O TYR A 567 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 575 through 579 removed outlier: 6.760A pdb=" N ILE A 592 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 667 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER A 640 " --> pdb=" O PHE A 665 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE A 665 " --> pdb=" O SER A 640 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1167 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: 3.19 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2200 1.33 - 1.45: 1399 1.45 - 1.57: 4832 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 8494 Sorted by residual: bond pdb=" F2 BEF A1301 " pdb="BE BEF A1301 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" F3 BEF A1301 " pdb="BE BEF A1301 " ideal model delta sigma weight residual 1.476 1.545 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" F1 BEF A1301 " pdb="BE BEF A1301 " ideal model delta sigma weight residual 1.476 1.534 -0.058 2.00e-02 2.50e+03 8.32e+00 bond pdb=" N VAL A 29 " pdb=" CA VAL A 29 " ideal model delta sigma weight residual 1.460 1.483 -0.023 1.19e-02 7.06e+03 3.79e+00 bond pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 1.524 1.548 -0.024 1.23e-02 6.61e+03 3.68e+00 ... (remaining 8489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 11421 2.54 - 5.07: 99 5.07 - 7.61: 7 7.61 - 10.15: 2 10.15 - 12.69: 1 Bond angle restraints: 11530 Sorted by residual: angle pdb=" N VAL A 29 " pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 110.53 117.37 -6.84 9.40e-01 1.13e+00 5.30e+01 angle pdb=" C LEU A 30 " pdb=" N PRO A 31 " pdb=" CA PRO A 31 " ideal model delta sigma weight residual 119.05 125.60 -6.55 1.11e+00 8.12e-01 3.48e+01 angle pdb=" N PRO A 34 " pdb=" CA PRO A 34 " pdb=" CB PRO A 34 " ideal model delta sigma weight residual 103.33 109.78 -6.45 1.10e+00 8.26e-01 3.44e+01 angle pdb=" F2 BEF A1301 " pdb="BE BEF A1301 " pdb=" F3 BEF A1301 " ideal model delta sigma weight residual 119.96 107.27 12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" N VAL A 198 " pdb=" CA VAL A 198 " pdb=" C VAL A 198 " ideal model delta sigma weight residual 113.42 108.96 4.46 1.17e+00 7.31e-01 1.45e+01 ... (remaining 11525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 4658 17.44 - 34.87: 370 34.87 - 52.31: 50 52.31 - 69.74: 6 69.74 - 87.18: 4 Dihedral angle restraints: 5088 sinusoidal: 1922 harmonic: 3166 Sorted by residual: dihedral pdb=" N PRO A 34 " pdb=" C PRO A 34 " pdb=" CA PRO A 34 " pdb=" CB PRO A 34 " ideal model delta harmonic sigma weight residual 115.10 123.28 -8.18 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" CB GLU A 420 " pdb=" CG GLU A 420 " pdb=" CD GLU A 420 " pdb=" OE1 GLU A 420 " ideal model delta sinusoidal sigma weight residual 0.00 -87.18 87.18 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CA TYR A 516 " pdb=" C TYR A 516 " pdb=" N SER A 517 " pdb=" CA SER A 517 " ideal model delta harmonic sigma weight residual -180.00 -164.24 -15.76 0 5.00e+00 4.00e-02 9.94e+00 ... (remaining 5085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1104 0.052 - 0.104: 219 0.104 - 0.156: 28 0.156 - 0.208: 1 0.208 - 0.260: 1 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CA PRO A 34 " pdb=" N PRO A 34 " pdb=" C PRO A 34 " pdb=" CB PRO A 34 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CG LEU A 73 " pdb=" CB LEU A 73 " pdb=" CD1 LEU A 73 " pdb=" CD2 LEU A 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CG LEU A 70 " pdb=" CB LEU A 70 " pdb=" CD1 LEU A 70 " pdb=" CD2 LEU A 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.15 2.00e-01 2.50e+01 6.01e-01 ... (remaining 1350 not shown) Planarity restraints: 1464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 74 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 75 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 29 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C VAL A 29 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 29 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 30 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 273 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO A 274 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " 0.022 5.00e-02 4.00e+02 ... (remaining 1461 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 28 2.43 - 3.05: 5188 3.05 - 3.67: 11571 3.67 - 4.28: 16319 4.28 - 4.90: 28499 Nonbonded interactions: 61605 Sorted by model distance: nonbonded pdb=" F1 BEF A1301 " pdb="MG MG A1302 " model vdw 1.814 2.120 nonbonded pdb=" OD2 ASP A 487 " pdb=" F1 BEF A1301 " model vdw 1.884 2.990 nonbonded pdb=" OD1 ASN A 987 " pdb=" NH1 ARG A1127 " model vdw 2.249 3.120 nonbonded pdb=" O THR A 489 " pdb="MG MG A1302 " model vdw 2.275 2.170 nonbonded pdb=" OG1 THR A 751 " pdb=" OE1 GLN A 778 " model vdw 2.276 3.040 ... (remaining 61600 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.570 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 8494 Z= 0.246 Angle : 0.606 12.687 11530 Z= 0.347 Chirality : 0.042 0.260 1353 Planarity : 0.004 0.041 1464 Dihedral : 12.442 87.180 3036 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % 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: -2.38 (0.23), residues: 1082 helix: -0.21 (0.22), residues: 490 sheet: -2.82 (0.38), residues: 131 loop : -2.73 (0.24), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1187 HIS 0.005 0.001 HIS A 672 PHE 0.014 0.001 PHE A 405 TYR 0.014 0.001 TYR A1057 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.894 Fit side-chains REVERT: A 695 MET cc_start: 0.8688 (ttm) cc_final: 0.8380 (ttm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1749 time to fit residues: 14.9263 Evaluate side-chains 35 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 0.0670 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 98 optimal weight: 0.8980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 166 HIS A 196 HIS A1050 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.080820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.060412 restraints weight = 23658.115| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.36 r_work: 0.2963 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8494 Z= 0.169 Angle : 0.520 8.505 11530 Z= 0.267 Chirality : 0.040 0.152 1353 Planarity : 0.004 0.041 1464 Dihedral : 4.066 16.099 1149 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.46 % Allowed : 8.87 % Favored : 90.67 % 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: -1.10 (0.25), residues: 1082 helix: 1.04 (0.24), residues: 490 sheet: -2.61 (0.37), residues: 145 loop : -2.10 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1187 HIS 0.008 0.001 HIS A 672 PHE 0.014 0.001 PHE A 226 TYR 0.010 0.001 TYR A1057 ARG 0.004 0.000 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 1.038 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 0.1496 time to fit residues: 10.8624 Evaluate side-chains 40 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 44 optimal weight: 0.0980 chunk 82 optimal weight: 6.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.077977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.057434 restraints weight = 24525.132| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.41 r_work: 0.2891 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8494 Z= 0.339 Angle : 0.575 7.592 11530 Z= 0.295 Chirality : 0.042 0.146 1353 Planarity : 0.003 0.041 1464 Dihedral : 4.288 16.417 1149 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.82 % Allowed : 11.26 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1082 helix: 1.50 (0.24), residues: 491 sheet: -2.46 (0.37), residues: 147 loop : -1.85 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1187 HIS 0.008 0.001 HIS A 672 PHE 0.018 0.001 PHE A 405 TYR 0.013 0.001 TYR A 516 ARG 0.003 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.909 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 50 average time/residue: 0.1490 time to fit residues: 12.4474 Evaluate side-chains 44 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 0.0060 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.080242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.059757 restraints weight = 23720.444| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.38 r_work: 0.2948 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8494 Z= 0.136 Angle : 0.502 9.477 11530 Z= 0.252 Chirality : 0.039 0.152 1353 Planarity : 0.003 0.039 1464 Dihedral : 4.006 16.063 1149 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.59 % Allowed : 12.51 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1082 helix: 1.80 (0.24), residues: 494 sheet: -2.09 (0.39), residues: 142 loop : -1.61 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1187 HIS 0.006 0.001 HIS A 672 PHE 0.025 0.001 PHE A 226 TYR 0.008 0.001 TYR A1057 ARG 0.002 0.000 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 1.038 Fit side-chains REVERT: A 813 MET cc_start: 0.8897 (tpt) cc_final: 0.8670 (tpt) outliers start: 14 outliers final: 10 residues processed: 48 average time/residue: 0.1555 time to fit residues: 12.5321 Evaluate side-chains 46 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 0.0000 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A1129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.079795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.059160 restraints weight = 23910.131| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.45 r_work: 0.2933 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8494 Z= 0.185 Angle : 0.515 12.047 11530 Z= 0.256 Chirality : 0.039 0.149 1353 Planarity : 0.003 0.039 1464 Dihedral : 3.962 15.759 1149 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.82 % Allowed : 12.97 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1082 helix: 1.98 (0.24), residues: 492 sheet: -2.00 (0.39), residues: 149 loop : -1.45 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1187 HIS 0.007 0.001 HIS A 672 PHE 0.017 0.001 PHE A 226 TYR 0.009 0.001 TYR A1057 ARG 0.002 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.959 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 51 average time/residue: 0.1465 time to fit residues: 12.4909 Evaluate side-chains 47 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 50.0000 chunk 60 optimal weight: 4.9990 chunk 2 optimal weight: 0.0170 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.079947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.059915 restraints weight = 23829.193| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.33 r_work: 0.2943 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8494 Z= 0.183 Angle : 0.517 11.029 11530 Z= 0.256 Chirality : 0.039 0.150 1353 Planarity : 0.003 0.038 1464 Dihedral : 3.957 15.790 1149 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.82 % Allowed : 13.88 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1082 helix: 2.11 (0.24), residues: 493 sheet: -1.75 (0.40), residues: 144 loop : -1.38 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1187 HIS 0.007 0.001 HIS A 672 PHE 0.019 0.001 PHE A 226 TYR 0.009 0.001 TYR A1057 ARG 0.001 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.940 Fit side-chains REVERT: A 72 MET cc_start: 0.7937 (tmm) cc_final: 0.7207 (tpp) REVERT: A 408 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8942 (mp) outliers start: 16 outliers final: 13 residues processed: 53 average time/residue: 0.1414 time to fit residues: 12.6402 Evaluate side-chains 51 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 35 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.080522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.060553 restraints weight = 23750.254| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.32 r_work: 0.2958 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8494 Z= 0.142 Angle : 0.498 10.475 11530 Z= 0.246 Chirality : 0.039 0.149 1353 Planarity : 0.003 0.038 1464 Dihedral : 3.861 15.909 1149 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.71 % Allowed : 13.99 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.26), residues: 1082 helix: 2.27 (0.24), residues: 488 sheet: -1.51 (0.41), residues: 144 loop : -1.24 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 787 HIS 0.006 0.001 HIS A 672 PHE 0.019 0.001 PHE A 226 TYR 0.008 0.001 TYR A1057 ARG 0.001 0.000 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 1.064 Fit side-chains REVERT: A 424 MET cc_start: 0.8802 (tmm) cc_final: 0.8416 (tmm) outliers start: 15 outliers final: 11 residues processed: 52 average time/residue: 0.1475 time to fit residues: 12.7366 Evaluate side-chains 49 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 6.9990 chunk 103 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 50.0000 chunk 24 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.080618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.060616 restraints weight = 23867.724| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.33 r_work: 0.2962 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8494 Z= 0.142 Angle : 0.500 10.248 11530 Z= 0.245 Chirality : 0.039 0.231 1353 Planarity : 0.003 0.038 1464 Dihedral : 3.816 15.722 1149 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.71 % Allowed : 14.45 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1082 helix: 2.31 (0.24), residues: 489 sheet: -1.32 (0.42), residues: 144 loop : -1.21 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 787 HIS 0.006 0.001 HIS A 672 PHE 0.019 0.001 PHE A 226 TYR 0.008 0.001 TYR A1057 ARG 0.001 0.000 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.931 Fit side-chains REVERT: A 72 MET cc_start: 0.7901 (tmm) cc_final: 0.7291 (tpp) REVERT: A 424 MET cc_start: 0.8838 (tmm) cc_final: 0.8299 (tmm) outliers start: 15 outliers final: 14 residues processed: 53 average time/residue: 0.1459 time to fit residues: 12.8450 Evaluate side-chains 53 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 86 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.079218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.058513 restraints weight = 24161.198| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.48 r_work: 0.2917 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8494 Z= 0.216 Angle : 0.522 10.055 11530 Z= 0.258 Chirality : 0.040 0.214 1353 Planarity : 0.003 0.038 1464 Dihedral : 3.940 16.527 1149 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.71 % Allowed : 14.56 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1082 helix: 2.30 (0.24), residues: 488 sheet: -1.30 (0.42), residues: 144 loop : -1.25 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1187 HIS 0.007 0.001 HIS A 672 PHE 0.020 0.001 PHE A 226 TYR 0.011 0.001 TYR A1057 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.934 Fit side-chains REVERT: A 72 MET cc_start: 0.8061 (tmm) cc_final: 0.7570 (tpp) outliers start: 15 outliers final: 15 residues processed: 51 average time/residue: 0.1489 time to fit residues: 12.6350 Evaluate side-chains 53 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.077000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.056900 restraints weight = 24062.102| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.31 r_work: 0.2877 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8494 Z= 0.404 Angle : 0.619 9.931 11530 Z= 0.312 Chirality : 0.043 0.202 1353 Planarity : 0.004 0.037 1464 Dihedral : 4.354 17.608 1149 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.71 % Allowed : 14.68 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1082 helix: 2.14 (0.24), residues: 484 sheet: -1.74 (0.42), residues: 139 loop : -1.32 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 137 HIS 0.009 0.001 HIS A 672 PHE 0.021 0.002 PHE A 405 TYR 0.015 0.002 TYR A1057 ARG 0.005 0.001 ARG A 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.906 Fit side-chains REVERT: A 72 MET cc_start: 0.8147 (tmm) cc_final: 0.7689 (tpp) REVERT: A 424 MET cc_start: 0.8718 (tmm) cc_final: 0.8090 (tmm) outliers start: 15 outliers final: 14 residues processed: 49 average time/residue: 0.1501 time to fit residues: 12.2971 Evaluate side-chains 50 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.079343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.059378 restraints weight = 23971.605| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.33 r_work: 0.2927 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8494 Z= 0.158 Angle : 0.519 9.692 11530 Z= 0.256 Chirality : 0.040 0.220 1353 Planarity : 0.003 0.038 1464 Dihedral : 4.068 16.643 1149 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.48 % Allowed : 15.02 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.26), residues: 1082 helix: 2.32 (0.24), residues: 487 sheet: -1.45 (0.44), residues: 131 loop : -1.21 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1187 HIS 0.006 0.001 HIS A 672 PHE 0.022 0.001 PHE A 226 TYR 0.009 0.001 TYR A1057 ARG 0.001 0.000 ARG A 634 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3154.55 seconds wall clock time: 56 minutes 55.79 seconds (3415.79 seconds total)