Starting phenix.real_space_refine on Fri Aug 22 16:23:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srm_40735/08_2025/8srm_40735.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srm_40735/08_2025/8srm_40735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8srm_40735/08_2025/8srm_40735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srm_40735/08_2025/8srm_40735.map" model { file = "/net/cci-nas-00/data/ceres_data/8srm_40735/08_2025/8srm_40735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srm_40735/08_2025/8srm_40735.cif" } resolution = 4.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.012 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: 3 Type Number sf(0) Gaussians C 3447 2.51 5 N 1163 2.21 5 O 1163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5773 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 2126 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 388} Link IDs: {'PTRANS': 12, 'TRANS': 415} Chain breaks: 3 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1407 Unresolved non-hydrogen angles: 1781 Unresolved non-hydrogen dihedrals: 1177 Unresolved non-hydrogen chiralities: 125 Planarities with less than four sites: {'TYR:plan': 11, 'PHE:plan': 21, 'ASN:plan1': 17, 'ASP:plan': 23, 'GLU:plan': 27, 'GLN:plan1': 23, 'HIS:plan': 11, 'ARG:plan': 25, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 748 Chain: "B" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1169 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 218} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 2 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 798 Unresolved non-hydrogen angles: 1006 Unresolved non-hydrogen dihedrals: 674 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'ASN:plan1': 6, 'TYR:plan': 6, 'GLN:plan1': 11, 'PHE:plan': 14, 'GLU:plan': 16, 'ASP:plan': 13, 'HIS:plan': 3, 'TRP:plan': 3, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 423 Chain: "C" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1015 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PTRANS': 2, 'TRANS': 202} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 627 Unresolved non-hydrogen angles: 795 Unresolved non-hydrogen dihedrals: 508 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'HIS:plan': 7, 'GLU:plan': 15, 'ARG:plan': 15, 'PHE:plan': 7, 'GLN:plan1': 16, 'TYR:plan': 4, 'ASP:plan': 7, 'TRP:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 340 Chain: "D" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1015 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PTRANS': 2, 'TRANS': 202} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 627 Unresolved non-hydrogen angles: 795 Unresolved non-hydrogen dihedrals: 508 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'HIS:plan': 7, 'GLU:plan': 15, 'ARG:plan': 15, 'PHE:plan': 7, 'GLN:plan1': 16, 'TYR:plan': 4, 'ASP:plan': 7, 'TRP:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 340 Chain: "E" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 224 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 4, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 2, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 96 Chain: "F" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 224 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 4, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 2, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 96 Time building chain proxies: 2.05, per 1000 atoms: 0.36 Number of scatterers: 5773 At special positions: 0 Unit cell: (178.4, 101.465, 160.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1163 8.00 N 1163 7.00 C 3447 6.00 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=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 527.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2242 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 83.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.842A pdb=" N LEU A 28 " --> pdb=" O THR A 24 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 127 through 202 removed outlier: 4.109A pdb=" N CYS A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 212 removed outlier: 3.647A pdb=" N SER A 212 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.719A pdb=" N GLN A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 320 through 335 Processing helix chain 'A' and resid 336 through 364 Proline residue: A 342 - end of helix removed outlier: 3.564A pdb=" N ILE A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 387 removed outlier: 3.878A pdb=" N ALA A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 490 removed outlier: 4.045A pdb=" N LYS A 429 " --> pdb=" O GLN A 425 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 543 removed outlier: 3.618A pdb=" N VAL A 501 " --> pdb=" O CYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 552 removed outlier: 3.953A pdb=" N LEU A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 589 Processing helix chain 'A' and resid 590 through 597 Proline residue: A 595 - end of helix Processing helix chain 'B' and resid 161 through 202 removed outlier: 4.473A pdb=" N LEU B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.956A pdb=" N ASP B 316 " --> pdb=" O ILE B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 335 Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 462 through 541 Proline residue: B 493 - end of helix Processing helix chain 'B' and resid 561 through 565 Processing helix chain 'B' and resid 578 through 589 Processing helix chain 'C' and resid 841 through 866 Processing helix chain 'C' and resid 869 through 873 Processing helix chain 'C' and resid 877 through 891 Processing helix chain 'C' and resid 891 through 923 Processing helix chain 'C' and resid 929 through 964 removed outlier: 4.819A pdb=" N ARG C 959 " --> pdb=" O LEU C 955 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE C 960 " --> pdb=" O ARG C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 971 Processing helix chain 'C' and resid 975 through 996 Processing helix chain 'C' and resid 1002 through 1020 Processing helix chain 'C' and resid 1023 through 1041 removed outlier: 4.298A pdb=" N ASN C1029 " --> pdb=" O ALA C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1044 No H-bonds generated for 'chain 'C' and resid 1042 through 1044' Processing helix chain 'D' and resid 841 through 866 removed outlier: 4.428A pdb=" N LEU D 847 " --> pdb=" O ILE D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 891 Processing helix chain 'D' and resid 891 through 915 removed outlier: 3.815A pdb=" N GLY D 895 " --> pdb=" O SER D 891 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 909 " --> pdb=" O LYS D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 923 Processing helix chain 'D' and resid 929 through 963 Processing helix chain 'D' and resid 964 through 970 Processing helix chain 'D' and resid 975 through 997 Processing helix chain 'D' and resid 999 through 1020 removed outlier: 3.956A pdb=" N CYS D1003 " --> pdb=" O HIS D 999 " (cutoff:3.500A) Proline residue: D1005 - end of helix Processing helix chain 'D' and resid 1023 through 1044 Processing helix chain 'E' and resid 463 through 471 removed outlier: 3.848A pdb=" N TYR E 467 " --> pdb=" O LEU E 463 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ARG E 468 " --> pdb=" O GLY E 464 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU E 469 " --> pdb=" O THR E 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 515 Proline residue: E 496 - end of helix removed outlier: 3.534A pdb=" N THR E 515 " --> pdb=" O ALA E 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 488 through 494 removed outlier: 4.183A pdb=" N SER F 494 " --> pdb=" O GLU F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 513 Processing helix chain 'F' and resid 514 through 516 No H-bonds generated for 'chain 'F' and resid 514 through 516' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 46 733 hydrogen bonds defined for protein. 2142 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: 1.01 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 1163 1.29 - 1.35: 1150 1.35 - 1.42: 0 1.42 - 1.49: 1163 1.49 - 1.56: 2284 Bond restraints: 5760 Sorted by residual: bond pdb=" CA PRO C 874 " pdb=" CB PRO C 874 " ideal model delta sigma weight residual 1.533 1.559 -0.025 1.42e-02 4.96e+03 3.22e+00 bond pdb=" CA PRO B 318 " pdb=" CB PRO B 318 " ideal model delta sigma weight residual 1.534 1.559 -0.025 1.40e-02 5.10e+03 3.17e+00 bond pdb=" C VAL B 492 " pdb=" O VAL B 492 " ideal model delta sigma weight residual 1.240 1.218 0.021 1.26e-02 6.30e+03 2.85e+00 bond pdb=" CA PRO B 590 " pdb=" CB PRO B 590 " ideal model delta sigma weight residual 1.534 1.557 -0.023 1.40e-02 5.10e+03 2.67e+00 bond pdb=" CA PRO A 493 " pdb=" CB PRO A 493 " ideal model delta sigma weight residual 1.533 1.554 -0.021 1.42e-02 4.96e+03 2.23e+00 ... (remaining 5755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 7726 1.13 - 2.27: 228 2.27 - 3.40: 47 3.40 - 4.53: 13 4.53 - 5.67: 4 Bond angle restraints: 8018 Sorted by residual: angle pdb=" N PRO B 559 " pdb=" CA PRO B 559 " pdb=" CB PRO B 559 " ideal model delta sigma weight residual 103.19 105.27 -2.08 5.60e-01 3.19e+00 1.39e+01 angle pdb=" N PRO E 474 " pdb=" CA PRO E 474 " pdb=" CB PRO E 474 " ideal model delta sigma weight residual 102.35 104.97 -2.62 7.10e-01 1.98e+00 1.36e+01 angle pdb=" C MET B 495 " pdb=" N TYR B 496 " pdb=" CA TYR B 496 " ideal model delta sigma weight residual 120.44 125.40 -4.96 1.36e+00 5.41e-01 1.33e+01 angle pdb=" CA VAL D1004 " pdb=" C VAL D1004 " pdb=" N PRO D1005 " ideal model delta sigma weight residual 120.83 118.65 2.18 6.10e-01 2.69e+00 1.27e+01 angle pdb=" C GLN B 494 " pdb=" N MET B 495 " pdb=" CA MET B 495 " ideal model delta sigma weight residual 120.28 125.05 -4.77 1.44e+00 4.82e-01 1.10e+01 ... (remaining 8013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 4.23: 3033 4.23 - 8.46: 307 8.46 - 12.69: 41 12.69 - 16.91: 9 16.91 - 21.14: 2 Dihedral angle restraints: 3392 sinusoidal: 0 harmonic: 3392 Sorted by residual: dihedral pdb=" CA GLN C 998 " pdb=" C GLN C 998 " pdb=" N HIS C 999 " pdb=" CA HIS C 999 " ideal model delta harmonic sigma weight residual 180.00 158.86 21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA SER B 490 " pdb=" C SER B 490 " pdb=" N THR B 491 " pdb=" CA THR B 491 " ideal model delta harmonic sigma weight residual 180.00 162.51 17.49 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ILE B 339 " pdb=" C ILE B 339 " pdb=" N ILE B 340 " pdb=" CA ILE B 340 " ideal model delta harmonic sigma weight residual -180.00 -163.54 -16.46 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 3389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 917 0.045 - 0.090: 185 0.090 - 0.134: 17 0.134 - 0.179: 1 0.179 - 0.224: 1 Chirality restraints: 1121 Sorted by residual: chirality pdb=" CA PRO B 595 " pdb=" N PRO B 595 " pdb=" C PRO B 595 " pdb=" CB PRO B 595 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA PRO B 493 " pdb=" N PRO B 493 " pdb=" C PRO B 493 " pdb=" CB PRO B 493 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA ILE A 577 " pdb=" N ILE A 577 " pdb=" C ILE A 577 " pdb=" CB ILE A 577 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1118 not shown) Planarity restraints: 1150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 497 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C CYS B 497 " 0.030 2.00e-02 2.50e+03 pdb=" O CYS B 497 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU B 498 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 487 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C GLU B 487 " 0.028 2.00e-02 2.50e+03 pdb=" O GLU B 487 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA B 488 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 545 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.51e+00 pdb=" C SER A 545 " -0.027 2.00e-02 2.50e+03 pdb=" O SER A 545 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 546 " 0.009 2.00e-02 2.50e+03 ... (remaining 1147 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1360 2.77 - 3.30: 6953 3.30 - 3.84: 10053 3.84 - 4.37: 9492 4.37 - 4.90: 14322 Nonbonded interactions: 42180 Sorted by model distance: nonbonded pdb=" O ASP C 969 " pdb=" N SER E 487 " model vdw 2.238 3.120 nonbonded pdb=" O PHE B 304 " pdb=" N LYS D 964 " model vdw 2.266 3.120 nonbonded pdb=" O ILE C 971 " pdb=" N SER E 487 " model vdw 2.322 3.120 nonbonded pdb=" O LEU B 547 " pdb=" N LEU B 551 " model vdw 2.325 3.120 nonbonded pdb=" O ASP B 336 " pdb=" N ARG B 341 " model vdw 2.341 3.120 ... (remaining 42175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 4.340 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.530 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.003 0.025 5760 Z= 0.220 Angle : 0.512 5.667 8018 Z= 0.376 Chirality : 0.034 0.224 1121 Planarity : 0.003 0.017 1150 Dihedral : 4.378 21.143 1150 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.25), residues: 1137 helix: 2.49 (0.17), residues: 838 sheet: None (None), residues: 0 loop : -0.65 (0.40), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 4 PHE 0.000 0.000 PHE A 6 TRP 0.000 0.000 TRP A 150 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 5760) covalent geometry : angle 0.51188 ( 8018) hydrogen bonds : bond 0.18702 ( 733) hydrogen bonds : angle 5.33585 ( 2142) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.227 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0278 time to fit residues: 1.5220 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.3114 r_free = 0.3114 target = 0.044262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.030928 restraints weight = 74534.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.030298 restraints weight = 60285.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.030149 restraints weight = 64776.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.030190 restraints weight = 59205.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.030237 restraints weight = 54984.244| |-----------------------------------------------------------------------------| r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5760 Z= 0.194 Angle : 0.391 3.744 8018 Z= 0.276 Chirality : 0.033 0.124 1121 Planarity : 0.003 0.015 1150 Dihedral : 4.252 19.051 1150 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.97 (0.25), residues: 1137 helix: 2.68 (0.16), residues: 874 sheet: None (None), residues: 0 loop : -0.60 (0.43), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 4 PHE 0.000 0.000 PHE A 6 TRP 0.000 0.000 TRP A 150 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 5760) covalent geometry : angle 0.39068 ( 8018) hydrogen bonds : bond 0.05433 ( 733) hydrogen bonds : angle 4.42871 ( 2142) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.236 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0276 time to fit residues: 1.5477 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 102 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 30.0000 chunk 94 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.3102 r_free = 0.3102 target = 0.043962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.030906 restraints weight = 74500.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.030229 restraints weight = 54912.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.030140 restraints weight = 55709.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.030181 restraints weight = 53972.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.030207 restraints weight = 51092.574| |-----------------------------------------------------------------------------| r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 5760 Z= 0.233 Angle : 0.403 4.903 8018 Z= 0.290 Chirality : 0.033 0.126 1121 Planarity : 0.002 0.012 1150 Dihedral : 4.294 20.091 1150 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.25), residues: 1137 helix: 2.54 (0.16), residues: 874 sheet: None (None), residues: 0 loop : -0.61 (0.43), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 4 PHE 0.000 0.000 PHE A 6 TRP 0.000 0.000 TRP A 150 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5760) covalent geometry : angle 0.40267 ( 8018) hydrogen bonds : bond 0.05121 ( 733) hydrogen bonds : angle 4.46309 ( 2142) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.169 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0243 time to fit residues: 1.3371 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 68 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 73 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- 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 = 0.3081 r_free = 0.3081 target = 0.043312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.030602 restraints weight = 75321.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.029881 restraints weight = 58279.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.029791 restraints weight = 62001.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.029814 restraints weight = 56010.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.029852 restraints weight = 52599.329| |-----------------------------------------------------------------------------| r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5760 Z= 0.313 Angle : 0.465 4.744 8018 Z= 0.344 Chirality : 0.034 0.125 1121 Planarity : 0.003 0.013 1150 Dihedral : 4.650 22.849 1150 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.25), residues: 1137 helix: 1.96 (0.16), residues: 870 sheet: None (None), residues: 0 loop : -0.80 (0.43), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 4 PHE 0.000 0.000 PHE A 6 TRP 0.000 0.000 TRP A 150 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 5760) covalent geometry : angle 0.46504 ( 8018) hydrogen bonds : bond 0.05539 ( 733) hydrogen bonds : angle 4.89713 ( 2142) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.224 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0262 time to fit residues: 1.4971 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 72 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 97 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 = 0.3113 r_free = 0.3113 target = 0.044251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.030939 restraints weight = 75550.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.030366 restraints weight = 56276.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.030252 restraints weight = 55840.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.030269 restraints weight = 55948.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.030298 restraints weight = 52887.195| |-----------------------------------------------------------------------------| r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 5760 Z= 0.164 Angle : 0.355 3.193 8018 Z= 0.249 Chirality : 0.033 0.128 1121 Planarity : 0.002 0.011 1150 Dihedral : 4.140 20.322 1150 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.10 (0.25), residues: 1137 helix: 2.87 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -0.97 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 4 PHE 0.000 0.000 PHE A 6 TRP 0.000 0.000 TRP A 150 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 5760) covalent geometry : angle 0.35522 ( 8018) hydrogen bonds : bond 0.04631 ( 733) hydrogen bonds : angle 4.13268 ( 2142) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.268 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0295 time to fit residues: 1.6858 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 2 optimal weight: 30.0000 chunk 106 optimal weight: 0.0670 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 83 optimal weight: 0.0980 chunk 98 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 overall best weight: 3.0324 ------------------------------------------------------------------------------- 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 = 0.3103 r_free = 0.3103 target = 0.043915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.030571 restraints weight = 73738.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.030011 restraints weight = 54036.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.029827 restraints weight = 63954.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.029857 restraints weight = 58284.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.029917 restraints weight = 55690.870| |-----------------------------------------------------------------------------| r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 5760 Z= 0.223 Angle : 0.389 4.333 8018 Z= 0.280 Chirality : 0.033 0.126 1121 Planarity : 0.002 0.010 1150 Dihedral : 4.187 20.388 1150 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.94 (0.25), residues: 1137 helix: 2.73 (0.17), residues: 872 sheet: None (None), residues: 0 loop : -0.90 (0.42), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 4 PHE 0.000 0.000 PHE A 6 TRP 0.000 0.000 TRP A 150 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5760) covalent geometry : angle 0.38891 ( 8018) hydrogen bonds : bond 0.04763 ( 733) hydrogen bonds : angle 4.31297 ( 2142) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.224 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0265 time to fit residues: 1.4919 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 83 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 30.0000 chunk 44 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3130 r_free = 0.3130 target = 0.044787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.030819 restraints weight = 72821.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.030497 restraints weight = 57953.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.030419 restraints weight = 55204.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.030447 restraints weight = 54022.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.030447 restraints weight = 52514.146| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 5760 Z= 0.120 Angle : 0.324 3.141 8018 Z= 0.221 Chirality : 0.032 0.127 1121 Planarity : 0.002 0.010 1150 Dihedral : 3.880 17.851 1150 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.67 (0.25), residues: 1137 helix: 3.34 (0.16), residues: 879 sheet: -3.85 (1.14), residues: 11 loop : -0.90 (0.43), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 4 PHE 0.000 0.000 PHE A 6 TRP 0.000 0.000 TRP A 150 Details of bonding type rmsd covalent geometry : bond 0.00153 ( 5760) covalent geometry : angle 0.32429 ( 8018) hydrogen bonds : bond 0.04145 ( 733) hydrogen bonds : angle 3.80330 ( 2142) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.210 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0260 time to fit residues: 1.4443 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 30.0000 chunk 46 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 chunk 34 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.3017 r_free = 0.3017 target = 0.041843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.025274 restraints weight = 68809.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.025353 restraints weight = 63741.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.025353 restraints weight = 60121.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.025353 restraints weight = 60121.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.025353 restraints weight = 60121.171| |-----------------------------------------------------------------------------| r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 5760 Z= 0.475 Angle : 0.601 7.288 8018 Z= 0.458 Chirality : 0.036 0.129 1121 Planarity : 0.004 0.015 1150 Dihedral : 4.873 23.055 1150 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.24), residues: 1137 helix: 1.29 (0.16), residues: 875 sheet: None (None), residues: 0 loop : -1.10 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 4 PHE 0.000 0.000 PHE A 6 TRP 0.000 0.000 TRP A 150 Details of bonding type rmsd covalent geometry : bond 0.00621 ( 5760) covalent geometry : angle 0.60068 ( 8018) hydrogen bonds : bond 0.06407 ( 733) hydrogen bonds : angle 5.42297 ( 2142) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.257 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0283 time to fit residues: 1.6207 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 102 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 86 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 = 0.3056 r_free = 0.3056 target = 0.043064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.026017 restraints weight = 72240.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.026088 restraints weight = 66352.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.026201 restraints weight = 63324.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.026201 restraints weight = 60114.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.026201 restraints weight = 60114.689| |-----------------------------------------------------------------------------| r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 5760 Z= 0.226 Angle : 0.400 4.094 8018 Z= 0.287 Chirality : 0.033 0.125 1121 Planarity : 0.002 0.012 1150 Dihedral : 4.496 21.594 1150 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.25), residues: 1137 helix: 2.12 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.12 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 4 PHE 0.000 0.000 PHE A 6 TRP 0.000 0.000 TRP A 150 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 5760) covalent geometry : angle 0.39997 ( 8018) hydrogen bonds : bond 0.05043 ( 733) hydrogen bonds : angle 4.55856 ( 2142) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.228 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0268 time to fit residues: 1.5091 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3029 r_free = 0.3029 target = 0.042105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.025257 restraints weight = 71303.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.025363 restraints weight = 66081.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.025451 restraints weight = 62312.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.025514 restraints weight = 58574.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.025555 restraints weight = 56932.499| |-----------------------------------------------------------------------------| r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 5760 Z= 0.389 Angle : 0.521 6.122 8018 Z= 0.391 Chirality : 0.035 0.123 1121 Planarity : 0.003 0.013 1150 Dihedral : 4.772 23.233 1150 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.25), residues: 1137 helix: 1.42 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -1.15 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 4 PHE 0.000 0.000 PHE A 6 TRP 0.000 0.000 TRP A 150 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 5760) covalent geometry : angle 0.52060 ( 8018) hydrogen bonds : bond 0.05851 ( 733) hydrogen bonds : angle 5.11621 ( 2142) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.228 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0261 time to fit residues: 1.4781 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 110 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3049 r_free = 0.3049 target = 0.042784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.025747 restraints weight = 71930.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.025857 restraints weight = 66493.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.025956 restraints weight = 62117.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.026007 restraints weight = 59550.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.026039 restraints weight = 57710.524| |-----------------------------------------------------------------------------| r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 5760 Z= 0.269 Angle : 0.427 4.716 8018 Z= 0.310 Chirality : 0.034 0.124 1121 Planarity : 0.003 0.012 1150 Dihedral : 4.581 22.265 1150 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.25), residues: 1137 helix: 1.90 (0.17), residues: 873 sheet: None (None), residues: 0 loop : -1.14 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 4 PHE 0.000 0.000 PHE A 6 TRP 0.000 0.000 TRP A 150 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 5760) covalent geometry : angle 0.42723 ( 8018) hydrogen bonds : bond 0.05224 ( 733) hydrogen bonds : angle 4.70950 ( 2142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1177.63 seconds wall clock time: 20 minutes 47.42 seconds (1247.42 seconds total)