Starting phenix.real_space_refine (version: dev) on Sun Feb 19 00:45:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6f_3063/02_2023/5a6f_3063_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6f_3063/02_2023/5a6f_3063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6f_3063/02_2023/5a6f_3063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6f_3063/02_2023/5a6f_3063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6f_3063/02_2023/5a6f_3063_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6f_3063/02_2023/5a6f_3063_trim.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 438": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 443": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 534": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 578": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 592": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 883": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8881 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 8666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8666 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 23, 'TRANS': 516} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 215 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'CIS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'UNK:plan-1': 43} Unresolved non-hydrogen planarities: 43 Time building chain proxies: 4.57, per 1000 atoms: 0.51 Number of scatterers: 8881 At special positions: 0 Unit cell: (80.08, 83.2, 82.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 O 837 8.00 N 772 7.00 C 2907 6.00 H 4330 1.00 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.08 Conformation dependent library (CDL) restraints added in 694.4 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1120 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 6 sheets defined 43.9% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'C' and resid 361 through 373 removed outlier: 3.565A pdb=" N LEU C 365 " --> pdb=" O LYS C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 399 removed outlier: 3.674A pdb=" N VAL C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 399 " --> pdb=" O VAL C 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 394 through 399' Processing helix chain 'C' and resid 417 through 424 removed outlier: 3.879A pdb=" N LEU C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 461 removed outlier: 4.059A pdb=" N ALA C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP C 447 " --> pdb=" O ARG C 443 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 479 removed outlier: 3.894A pdb=" N PHE C 477 " --> pdb=" O GLU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 499 Processing helix chain 'C' and resid 504 through 513 removed outlier: 3.572A pdb=" N LEU C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 509 " --> pdb=" O THR C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 535 removed outlier: 3.529A pdb=" N CYS C 535 " --> pdb=" O MET C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 567 removed outlier: 3.951A pdb=" N ALA C 562 " --> pdb=" O SER C 558 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA C 563 " --> pdb=" O PHE C 559 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE C 564 " --> pdb=" O THR C 560 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS C 565 " --> pdb=" O TYR C 561 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS C 567 " --> pdb=" O ALA C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 792 removed outlier: 4.143A pdb=" N TYR C 788 " --> pdb=" O GLY C 784 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN C 789 " --> pdb=" O ASN C 785 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 792 " --> pdb=" O TYR C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.806A pdb=" N LEU C 820 " --> pdb=" O GLU C 816 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 821 " --> pdb=" O HIS C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 838 through 844 Processing helix chain 'C' and resid 867 through 870 Processing helix chain 'C' and resid 871 through 885 removed outlier: 3.689A pdb=" N ILE C 875 " --> pdb=" O ASP C 871 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN C 877 " --> pdb=" O LYS C 873 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR C 880 " --> pdb=" O VAL C 876 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N MET C 881 " --> pdb=" O ASN C 877 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 882 " --> pdb=" O VAL C 878 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 883 " --> pdb=" O GLN C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 903 removed outlier: 4.401A pdb=" N ARG C 901 " --> pdb=" O SER C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 924 removed outlier: 4.602A pdb=" N SER C 916 " --> pdb=" O SER C 912 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS C 917 " --> pdb=" O LEU C 913 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C 918 " --> pdb=" O ALA C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 934 through 939 Processing helix chain 'C' and resid 945 through 956 removed outlier: 3.785A pdb=" N ASP C 949 " --> pdb=" O ILE C 945 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR C 950 " --> pdb=" O SER C 946 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU C 951 " --> pdb=" O MET C 947 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 953 " --> pdb=" O ASP C 949 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 970 removed outlier: 3.569A pdb=" N ILE C 964 " --> pdb=" O TYR C 960 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR C 965 " --> pdb=" O MET C 961 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG C 966 " --> pdb=" O ILE C 962 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 967 " --> pdb=" O THR C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 992 Processing helix chain 'C' and resid 995 through 1003 removed outlier: 3.641A pdb=" N LYS C1001 " --> pdb=" O ARG C 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1081 through 1098 removed outlier: 3.764A pdb=" N UNK D1088 " --> pdb=" O UNK D1084 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N UNK D1097 " --> pdb=" O UNK D1093 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1113 removed outlier: 3.655A pdb=" N UNK D1110 " --> pdb=" O UNK D1106 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N UNK D1111 " --> pdb=" O UNK D1107 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N UNK D1112 " --> pdb=" O UNK D1108 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N UNK D1113 " --> pdb=" O UNK D1109 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'C' and resid 408 through 412 removed outlier: 3.598A pdb=" N CYS C 387 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA C 431 " --> pdb=" O HIS C 352 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'C' and resid 467 through 470 removed outlier: 3.588A pdb=" N VAL C 468 " --> pdb=" O HIS C 484 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.664A pdb=" N TYR C 603 " --> pdb=" O TYR C 541 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS C 573 " --> pdb=" O ILE C 604 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'C' and resid 829 through 833 removed outlier: 3.711A pdb=" N LEU C 811 " --> pdb=" O MET C 832 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 780 " --> pdb=" O LEU C 810 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 777 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 855 " --> pdb=" O ILE C 891 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU C 893 " --> pdb=" O VAL C 855 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 894 " --> pdb=" O PHE C 943 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'C' and resid 979 through 984 removed outlier: 3.638A pdb=" N VAL C1162 " --> pdb=" O MET C 983 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE C1009 " --> pdb=" O ILE C1165 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'C' and resid 1012 through 1013 removed outlier: 3.749A pdb=" N LEU C1147 " --> pdb=" O ILE C1013 " (cutoff:3.500A) 138 hydrogen bonds defined for protein. 378 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: 2.73 Time building geometry restraints manager: 6.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 4314 1.05 - 1.26: 756 1.26 - 1.46: 1632 1.46 - 1.67: 2216 1.67 - 1.88: 54 Bond restraints: 8972 Sorted by residual: bond pdb=" CA VAL C 441 " pdb=" CB VAL C 441 " ideal model delta sigma weight residual 1.540 1.590 -0.050 1.17e-02 7.31e+03 1.85e+01 bond pdb=" CA ILE C 401 " pdb=" C ILE C 401 " ideal model delta sigma weight residual 1.524 1.562 -0.038 9.30e-03 1.16e+04 1.68e+01 bond pdb=" CA THR C1142 " pdb=" C THR C1142 " ideal model delta sigma weight residual 1.522 1.574 -0.052 1.27e-02 6.20e+03 1.66e+01 bond pdb=" N LEU C1143 " pdb=" CA LEU C1143 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.14e-02 7.69e+03 1.63e+01 bond pdb=" CA ASN C 611 " pdb=" C ASN C 611 " ideal model delta sigma weight residual 1.523 1.576 -0.053 1.35e-02 5.49e+03 1.54e+01 ... (remaining 8967 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.04: 127 106.04 - 113.07: 10247 113.07 - 120.11: 2892 120.11 - 127.14: 2813 127.14 - 134.18: 42 Bond angle restraints: 16121 Sorted by residual: angle pdb=" N MET C 828 " pdb=" CA MET C 828 " pdb=" C MET C 828 " ideal model delta sigma weight residual 110.91 122.62 -11.71 1.17e+00 7.31e-01 1.00e+02 angle pdb=" N GLY C 970 " pdb=" CA GLY C 970 " pdb=" C GLY C 970 " ideal model delta sigma weight residual 110.29 99.44 10.85 1.28e+00 6.10e-01 7.19e+01 angle pdb=" N ASN C 785 " pdb=" CA ASN C 785 " pdb=" C ASN C 785 " ideal model delta sigma weight residual 112.87 104.14 8.73 1.20e+00 6.94e-01 5.29e+01 angle pdb=" C PHE C 826 " pdb=" N PRO C 827 " pdb=" CA PRO C 827 " ideal model delta sigma weight residual 120.85 113.38 7.47 1.08e+00 8.57e-01 4.79e+01 angle pdb=" O PRO C1150 " pdb=" C PRO C1150 " pdb=" N PRO C1151 " ideal model delta sigma weight residual 121.15 123.98 -2.83 4.70e-01 4.53e+00 3.63e+01 ... (remaining 16116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 3347 15.20 - 30.39: 212 30.39 - 45.59: 52 45.59 - 60.79: 72 60.79 - 75.98: 1 Dihedral angle restraints: 3684 sinusoidal: 1663 harmonic: 2021 Sorted by residual: dihedral pdb=" CA LEU C 969 " pdb=" C LEU C 969 " pdb=" N GLY C 970 " pdb=" CA GLY C 970 " ideal model delta harmonic sigma weight residual -180.00 -149.36 -30.64 0 5.00e+00 4.00e-02 3.75e+01 dihedral pdb=" CA THR C 974 " pdb=" C THR C 974 " pdb=" N PRO C 975 " pdb=" CA PRO C 975 " ideal model delta harmonic sigma weight residual -180.00 -155.89 -24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA TYR C 831 " pdb=" C TYR C 831 " pdb=" N MET C 832 " pdb=" CA MET C 832 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 3681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 407 0.036 - 0.073: 203 0.073 - 0.109: 72 0.109 - 0.145: 24 0.145 - 0.181: 10 Chirality restraints: 716 Sorted by residual: chirality pdb=" CA ASN C 785 " pdb=" N ASN C 785 " pdb=" C ASN C 785 " pdb=" CB ASN C 785 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CA MET C 828 " pdb=" N MET C 828 " pdb=" C MET C 828 " pdb=" CB MET C 828 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CA ILE C1013 " pdb=" N ILE C1013 " pdb=" C ILE C1013 " pdb=" CB ILE C1013 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.66e-01 ... (remaining 713 not shown) Planarity restraints: 1315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 826 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.54e+00 pdb=" N PRO C 827 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 827 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 827 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 785 " 0.004 2.00e-02 2.50e+03 2.16e-02 7.03e+00 pdb=" CG ASN C 785 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN C 785 " -0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN C 785 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN C 785 " -0.028 2.00e-02 2.50e+03 pdb="HD22 ASN C 785 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C1149 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO C1150 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C1150 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C1150 " 0.031 5.00e-02 4.00e+02 ... (remaining 1312 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.01: 107 2.01 - 2.66: 11951 2.66 - 3.31: 24323 3.31 - 3.95: 29332 3.95 - 4.60: 46619 Nonbonded interactions: 112332 Sorted by model distance: nonbonded pdb=" H PHE C 550 " pdb=" OE2 GLU C 609 " model vdw 1.366 1.850 nonbonded pdb=" HG CYS C1003 " pdb=" O GLU C1008 " model vdw 1.563 2.620 nonbonded pdb=" H ILE C 575 " pdb=" O PHE C 602 " model vdw 1.581 1.850 nonbonded pdb=" HZ3 LYS C 549 " pdb=" O SER C 612 " model vdw 1.583 1.850 nonbonded pdb=" O SER C 612 " pdb=" HG SER C 612 " model vdw 1.595 1.850 ... (remaining 112327 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 35 5.16 5 C 2907 2.51 5 N 772 2.21 5 O 837 1.98 5 H 4330 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.160 Extract box with map and model: 4.090 Check model and map are aligned: 0.130 Process input model: 28.990 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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 : 0.012 0.090 4642 Z= 0.776 Angle : 1.505 11.710 6286 Z= 0.980 Chirality : 0.052 0.181 716 Planarity : 0.007 0.073 802 Dihedral : 12.322 75.983 1697 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.22 % Favored : 87.59 % Rotamer Outliers : 3.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.26), residues: 532 helix: -4.54 (0.18), residues: 143 sheet: -1.55 (0.48), residues: 85 loop : -3.26 (0.27), residues: 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 600 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 67 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 83 average time/residue: 0.3711 time to fit residues: 38.9201 Evaluate side-chains 53 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1124 time to fit residues: 2.1262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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: 0.7360 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 4642 Z= 0.224 Angle : 0.662 5.147 6286 Z= 0.356 Chirality : 0.040 0.139 716 Planarity : 0.006 0.057 802 Dihedral : 6.206 23.278 635 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.29), residues: 532 helix: -3.64 (0.24), residues: 151 sheet: -1.04 (0.50), residues: 92 loop : -2.67 (0.30), residues: 289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 600 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.3872 time to fit residues: 24.8527 Evaluate side-chains 39 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 52 optimal weight: 0.0270 chunk 57 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 17 optimal weight: 0.0970 chunk 42 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 overall best weight: 5.4242 ------------------------------------------------------------------------------- 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: 0.7394 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 4642 Z= 0.237 Angle : 0.579 5.093 6286 Z= 0.310 Chirality : 0.038 0.140 716 Planarity : 0.005 0.054 802 Dihedral : 5.329 17.740 635 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.31), residues: 532 helix: -2.54 (0.32), residues: 153 sheet: -1.13 (0.48), residues: 109 loop : -2.21 (0.33), residues: 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 600 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 42 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.4162 time to fit residues: 22.6031 Evaluate side-chains 37 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 25 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 overall best weight: 3.2386 ------------------------------------------------------------------------------- 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: 0.7345 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 4642 Z= 0.164 Angle : 0.509 5.061 6286 Z= 0.264 Chirality : 0.038 0.139 716 Planarity : 0.005 0.050 802 Dihedral : 4.906 17.147 635 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.33), residues: 532 helix: -1.69 (0.35), residues: 162 sheet: -0.96 (0.48), residues: 109 loop : -1.85 (0.36), residues: 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 600 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.4130 time to fit residues: 21.3097 Evaluate side-chains 37 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.725 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 overall best weight: 5.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 542 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 4642 Z= 0.241 Angle : 0.531 4.966 6286 Z= 0.279 Chirality : 0.037 0.138 716 Planarity : 0.005 0.052 802 Dihedral : 4.667 15.145 635 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.35), residues: 532 helix: -1.51 (0.34), residues: 175 sheet: -1.04 (0.47), residues: 119 loop : -1.56 (0.41), residues: 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 600 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.3977 time to fit residues: 21.0504 Evaluate side-chains 37 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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: 0.7346 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 4642 Z= 0.208 Angle : 0.511 4.989 6286 Z= 0.268 Chirality : 0.038 0.136 716 Planarity : 0.005 0.050 802 Dihedral : 4.526 15.910 635 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.36), residues: 532 helix: -1.13 (0.36), residues: 176 sheet: -0.89 (0.48), residues: 119 loop : -1.38 (0.41), residues: 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 600 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.3915 time to fit residues: 20.8569 Evaluate side-chains 36 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.700 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 4642 Z= 0.130 Angle : 0.476 4.928 6286 Z= 0.243 Chirality : 0.039 0.143 716 Planarity : 0.004 0.054 802 Dihedral : 4.238 15.314 635 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.37), residues: 532 helix: -0.48 (0.38), residues: 176 sheet: -0.69 (0.50), residues: 109 loop : -1.04 (0.42), residues: 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 600 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 42 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.3973 time to fit residues: 21.3339 Evaluate side-chains 37 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 904 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 4642 Z= 0.175 Angle : 0.478 4.904 6286 Z= 0.248 Chirality : 0.037 0.136 716 Planarity : 0.004 0.042 802 Dihedral : 4.187 14.874 635 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.37), residues: 532 helix: -0.50 (0.38), residues: 178 sheet: -0.78 (0.48), residues: 117 loop : -1.05 (0.42), residues: 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 600 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 43 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.3997 time to fit residues: 22.1473 Evaluate side-chains 38 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 0.0170 chunk 34 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 57 optimal weight: 30.0000 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- 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: 0.7277 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 4642 Z= 0.123 Angle : 0.459 4.900 6286 Z= 0.230 Chirality : 0.038 0.142 716 Planarity : 0.004 0.038 802 Dihedral : 3.980 15.134 635 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.38), residues: 532 helix: -0.19 (0.39), residues: 178 sheet: -0.48 (0.50), residues: 107 loop : -0.83 (0.44), residues: 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 600 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 42 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.4006 time to fit residues: 21.6459 Evaluate side-chains 36 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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: 0.7314 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 4642 Z= 0.203 Angle : 0.494 4.848 6286 Z= 0.253 Chirality : 0.037 0.135 716 Planarity : 0.004 0.040 802 Dihedral : 4.068 14.371 635 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.12 (0.37), residues: 532 helix: -0.47 (0.37), residues: 181 sheet: -0.67 (0.48), residues: 117 loop : -0.83 (0.44), residues: 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 600 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.4608 time to fit residues: 24.3725 Evaluate side-chains 36 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.650 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 33 optimal weight: 0.0010 chunk 52 optimal weight: 0.2980 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.2592 ------------------------------------------------------------------------------- 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 = 0.3121 r_free = 0.3121 target = 0.044655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.038472 restraints weight = 118925.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.039968 restraints weight = 59289.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.041029 restraints weight = 35023.925| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 4642 Z= 0.118 Angle : 0.450 4.887 6286 Z= 0.224 Chirality : 0.038 0.141 716 Planarity : 0.004 0.035 802 Dihedral : 3.872 14.718 635 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.38), residues: 532 helix: -0.13 (0.39), residues: 182 sheet: -0.65 (0.48), residues: 117 loop : -0.58 (0.46), residues: 233 =============================================================================== Job complete usr+sys time: 2274.12 seconds wall clock time: 41 minutes 13.44 seconds (2473.44 seconds total)