Starting phenix.real_space_refine on Thu Nov 14 10:46:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srm_40735/11_2024/8srm_40735.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srm_40735/11_2024/8srm_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srm_40735/11_2024/8srm_40735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srm_40735/11_2024/8srm_40735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srm_40735/11_2024/8srm_40735.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srm_40735/11_2024/8srm_40735.cif" } resolution = 4.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLN:plan1': 23, 'ARG:plan': 25, 'TYR:plan': 11, 'ASN:plan1': 17, 'TRP:plan': 5, 'ASP:plan': 23, 'PHE:plan': 21, 'GLU:plan': 27, 'HIS:plan': 11} 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: {'GLN:plan1': 11, 'ARG:plan': 18, 'TYR:plan': 6, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 16, 'HIS:plan': 3} 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: {'GLN:plan1': 16, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 15, 'ARG:plan': 15} 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: {'GLN:plan1': 16, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 15, 'ARG:plan': 15} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 96 Time building chain proxies: 4.76, per 1000 atoms: 0.82 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: 1.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.47 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: 1.81 Time building geometry restraints manager: 2.04 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: 0.010 Normalize map: mean=0, sd=1: 1.930 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.140 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.490 ------------------------------------------------------------------------------- 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= 0.210 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 (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: 2.57 (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 TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** 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 : 0.646 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0568 time to fit residues: 3.4851 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 : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 88 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5760 Z= 0.380 Angle : 0.535 4.298 8018 Z= 0.401 Chirality : 0.035 0.119 1121 Planarity : 0.004 0.017 1150 Dihedral : 4.708 21.471 1150 Min Nonbonded Distance : 2.454 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.24), residues: 1137 helix: 1.61 (0.16), residues: 872 sheet: None (None), residues: 0 loop : -0.83 (0.42), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** 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 : 0.621 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0541 time to fit residues: 3.4336 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 : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 5760 Z= 0.270 Angle : 0.442 4.854 8018 Z= 0.322 Chirality : 0.034 0.123 1121 Planarity : 0.003 0.014 1150 Dihedral : 4.612 22.215 1150 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 0.84 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 (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: 1.83 (0.25), residues: 1137 helix: 1.81 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -0.78 (0.43), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** 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 : 0.718 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0540 time to fit residues: 3.4240 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 : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.0980 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1406 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= 0.177 Angle : 0.371 3.322 8018 Z= 0.262 Chirality : 0.033 0.126 1121 Planarity : 0.002 0.012 1150 Dihedral : 4.314 20.943 1150 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.48 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 (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: 2.62 (0.25), residues: 1137 helix: 2.46 (0.17), residues: 877 sheet: None (None), residues: 0 loop : -0.91 (0.43), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** 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 : 0.664 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0556 time to fit residues: 3.4155 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 : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.2980 chunk 1 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5760 Z= 0.367 Angle : 0.522 6.115 8018 Z= 0.392 Chirality : 0.035 0.120 1121 Planarity : 0.003 0.013 1150 Dihedral : 4.830 23.348 1150 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % 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 (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: 1.42 (0.25), residues: 1137 helix: 1.53 (0.17), residues: 869 sheet: None (None), residues: 0 loop : -0.94 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** 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 : 0.662 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0551 time to fit residues: 3.4938 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 : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 5760 Z= 0.326 Angle : 0.484 4.840 8018 Z= 0.360 Chirality : 0.034 0.122 1121 Planarity : 0.003 0.013 1150 Dihedral : 4.852 23.335 1150 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.08 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 (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: 1.18 (0.25), residues: 1137 helix: 1.38 (0.17), residues: 873 sheet: None (None), residues: 0 loop : -1.14 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** 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 : 0.679 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0547 time to fit residues: 3.4182 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 : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 5760 Z= 0.304 Angle : 0.470 5.148 8018 Z= 0.346 Chirality : 0.034 0.125 1121 Planarity : 0.003 0.012 1150 Dihedral : 4.799 23.545 1150 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % 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 (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: 1.29 (0.25), residues: 1137 helix: 1.47 (0.17), residues: 870 sheet: None (None), residues: 0 loop : -1.15 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** 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 : 0.543 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0547 time to fit residues: 3.2563 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 : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1991 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= 0.253 Angle : 0.426 4.693 8018 Z= 0.309 Chirality : 0.034 0.125 1121 Planarity : 0.003 0.012 1150 Dihedral : 4.638 22.514 1150 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % 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 (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: 1.73 (0.25), residues: 1137 helix: 1.82 (0.17), residues: 873 sheet: None (None), residues: 0 loop : -1.13 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** 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 : 0.653 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0627 time to fit residues: 3.6302 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 : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.3980 chunk 104 optimal weight: 7.9990 chunk 61 optimal weight: 0.0050 chunk 44 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.013 5760 Z= 0.096 Angle : 0.324 3.362 8018 Z= 0.217 Chirality : 0.033 0.129 1121 Planarity : 0.002 0.011 1150 Dihedral : 4.039 18.268 1150 Min Nonbonded Distance : 2.615 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.25), residues: 1137 helix: 3.00 (0.16), residues: 891 sheet: -4.04 (1.09), residues: 11 loop : -1.17 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** 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 : 0.625 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0515 time to fit residues: 3.2810 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 : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5760 Z= 0.305 Angle : 0.466 6.094 8018 Z= 0.345 Chirality : 0.034 0.124 1121 Planarity : 0.003 0.012 1150 Dihedral : 4.381 21.137 1150 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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 (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: 2.28 (0.25), residues: 1137 helix: 2.23 (0.17), residues: 879 sheet: None (None), residues: 0 loop : -1.13 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 ********************** 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 : 0.682 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0556 time to fit residues: 3.4844 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 : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3019 r_free = 0.3019 target = 0.041846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.025285 restraints weight = 68867.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.025288 restraints weight = 63531.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.025288 restraints weight = 63384.831| |-----------------------------------------------------------------------------| r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 5760 Z= 0.403 Angle : 0.556 6.720 8018 Z= 0.417 Chirality : 0.035 0.117 1121 Planarity : 0.004 0.014 1150 Dihedral : 5.020 24.345 1150 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % 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 (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: 0.75 (0.24), residues: 1137 helix: 1.07 (0.16), residues: 875 sheet: None (None), residues: 0 loop : -1.32 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1006.89 seconds wall clock time: 19 minutes 2.16 seconds (1142.16 seconds total)