Starting phenix.real_space_refine on Fri Dec 8 20:23:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6f_3063/12_2023/5a6f_3063_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6f_3063/12_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_3063/12_2023/5a6f_3063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6f_3063/12_2023/5a6f_3063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6f_3063/12_2023/5a6f_3063_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6f_3063/12_2023/5a6f_3063_trim.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. 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-1.21rc1-5172/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: 5.20, per 1000 atoms: 0.59 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: 7.07 Conformation dependent library (CDL) restraints added in 843.1 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: 0.82 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: 3.08 Time building geometry restraints manager: 7.34 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: 3802 15.20 - 30.39: 231 30.39 - 45.59: 71 45.59 - 60.79: 75 60.79 - 75.98: 1 Dihedral angle restraints: 4180 sinusoidal: 2159 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 4177 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.140 Extract box with map and model: 3.830 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 32.770 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 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 % Allowed : 8.11 % Favored : 88.15 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 528 HIS 0.010 0.002 HIS C 478 PHE 0.018 0.003 PHE C 564 TYR 0.033 0.003 TYR C 788 ARG 0.004 0.001 ARG C 901 *********************** 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 : 0.764 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: 0.3738 time to fit residues: 39.2381 Evaluate side-chains 53 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0990 time to fit residues: 1.9948 ------------------------------------------------------------------------------- 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: 3.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 0.0870 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 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: 4.4166 ------------------------------------------------------------------------------- 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: 0.7755 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4642 Z= 0.244 Angle : 0.679 5.314 6286 Z= 0.366 Chirality : 0.041 0.136 716 Planarity : 0.006 0.060 802 Dihedral : 6.264 24.136 635 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.28), residues: 532 helix: -3.76 (0.23), residues: 156 sheet: -1.14 (0.49), residues: 93 loop : -2.78 (0.30), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 528 HIS 0.005 0.001 HIS C 478 PHE 0.016 0.002 PHE C 368 TYR 0.017 0.002 TYR C 532 ARG 0.011 0.001 ARG C 934 *********************** 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 : 0.801 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 outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.4100 time to fit residues: 26.0536 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: 0.9732 ------------------------------------------------------------------------------- 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: 20.0000 chunk 43 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 896 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 4642 Z= 0.254 Angle : 0.596 5.242 6286 Z= 0.318 Chirality : 0.039 0.138 716 Planarity : 0.005 0.052 802 Dihedral : 5.250 17.145 635 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -2.94 (0.32), residues: 532 helix: -2.38 (0.33), residues: 151 sheet: -1.11 (0.48), residues: 108 loop : -2.01 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 404 HIS 0.007 0.002 HIS C 514 PHE 0.014 0.002 PHE C 368 TYR 0.023 0.002 TYR C 373 ARG 0.004 0.000 ARG C 795 *********************** 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 43 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.828 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: 0.3861 time to fit residues: 21.4792 Evaluate side-chains 37 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9908 ------------------------------------------------------------------------------- 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: 20.0000 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 46 optimal weight: 30.0000 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.7750 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 4642 Z= 0.246 Angle : 0.558 5.088 6286 Z= 0.295 Chirality : 0.038 0.138 716 Planarity : 0.005 0.059 802 Dihedral : 4.931 17.579 635 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.34), residues: 532 helix: -1.69 (0.34), residues: 172 sheet: -1.18 (0.47), residues: 119 loop : -1.70 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 528 HIS 0.004 0.001 HIS C 593 PHE 0.014 0.002 PHE C 931 TYR 0.021 0.002 TYR C 831 ARG 0.002 0.000 ARG C 517 *********************** 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 43 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.776 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: 43 average time/residue: 0.3819 time to fit residues: 21.4118 Evaluate side-chains 37 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.758 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9428 ------------------------------------------------------------------------------- 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: 10.0000 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- 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: 0.7719 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4642 Z= 0.201 Angle : 0.509 5.007 6286 Z= 0.266 Chirality : 0.038 0.139 716 Planarity : 0.005 0.052 802 Dihedral : 4.631 15.435 635 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -2.03 (0.35), residues: 532 helix: -1.30 (0.35), residues: 174 sheet: -1.10 (0.48), residues: 119 loop : -1.36 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 455 HIS 0.004 0.001 HIS C 542 PHE 0.011 0.002 PHE C 368 TYR 0.011 0.001 TYR C 788 ARG 0.004 0.000 ARG C 397 *********************** 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 42 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.695 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 outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.4173 time to fit residues: 22.3669 Evaluate side-chains 37 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9467 ------------------------------------------------------------------------------- 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: 9.9990 chunk 56 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 40 optimal weight: 20.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- 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: 0.7709 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4642 Z= 0.208 Angle : 0.517 4.980 6286 Z= 0.271 Chirality : 0.037 0.150 716 Planarity : 0.005 0.048 802 Dihedral : 4.505 15.484 635 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: -1.72 (0.36), residues: 532 helix: -1.09 (0.37), residues: 168 sheet: -0.99 (0.49), residues: 119 loop : -1.10 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 455 HIS 0.004 0.001 HIS C 448 PHE 0.011 0.001 PHE C 368 TYR 0.020 0.001 TYR C 831 ARG 0.003 0.000 ARG C 544 *********************** 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 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.666 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: 0 outliers final: 0 residues processed: 40 average time/residue: 0.4092 time to fit residues: 20.7210 Evaluate side-chains 37 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8273 ------------------------------------------------------------------------------- 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: 10.0000 chunk 47 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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: 0.7727 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 4642 Z= 0.283 Angle : 0.572 5.045 6286 Z= 0.306 Chirality : 0.037 0.139 716 Planarity : 0.005 0.048 802 Dihedral : 4.614 15.423 635 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -1.98 (0.35), residues: 532 helix: -1.43 (0.35), residues: 167 sheet: -1.11 (0.48), residues: 118 loop : -1.18 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 404 HIS 0.005 0.002 HIS C 593 PHE 0.016 0.002 PHE C 368 TYR 0.016 0.002 TYR C 788 ARG 0.004 0.001 ARG C 934 *********************** 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 39 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 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 revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.4675 time to fit residues: 23.1560 Evaluate side-chains 36 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8676 ------------------------------------------------------------------------------- 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: 2.9990 chunk 43 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.6170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4642 Z= 0.220 Angle : 0.519 4.997 6286 Z= 0.272 Chirality : 0.037 0.133 716 Planarity : 0.004 0.045 802 Dihedral : 4.452 15.783 635 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -1.77 (0.36), residues: 532 helix: -1.17 (0.36), residues: 171 sheet: -0.90 (0.52), residues: 101 loop : -1.18 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 455 HIS 0.004 0.001 HIS C 565 PHE 0.011 0.002 PHE C 931 TYR 0.015 0.001 TYR C 788 ARG 0.003 0.000 ARG C 544 *********************** 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 39 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.694 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: 39 average time/residue: 0.4455 time to fit residues: 21.8176 Evaluate side-chains 35 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.789 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8700 ------------------------------------------------------------------------------- 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: 0.9990 chunk 49 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 33 optimal weight: 0.0870 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 57 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- 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: 0.7660 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4642 Z= 0.155 Angle : 0.476 4.946 6286 Z= 0.245 Chirality : 0.038 0.137 716 Planarity : 0.004 0.039 802 Dihedral : 4.255 16.079 635 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -1.37 (0.37), residues: 532 helix: -0.74 (0.38), residues: 172 sheet: -0.84 (0.51), residues: 102 loop : -0.93 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 455 HIS 0.003 0.001 HIS C 565 PHE 0.011 0.001 PHE C 933 TYR 0.011 0.001 TYR C 788 ARG 0.003 0.000 ARG C 934 *********************** 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 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.752 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 outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.4367 time to fit residues: 22.0589 Evaluate side-chains 34 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.753 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9350 ------------------------------------------------------------------------------- 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: 7.9990 chunk 28 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 514 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.6402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4642 Z= 0.200 Angle : 0.502 4.931 6286 Z= 0.257 Chirality : 0.037 0.134 716 Planarity : 0.004 0.038 802 Dihedral : 4.272 15.754 635 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.35 (0.37), residues: 532 helix: -0.78 (0.38), residues: 172 sheet: -0.77 (0.51), residues: 102 loop : -0.90 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 455 HIS 0.004 0.001 HIS C 565 PHE 0.010 0.002 PHE C 368 TYR 0.012 0.001 TYR C 788 ARG 0.001 0.000 ARG C 397 ********************** 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 40 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.783 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 outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.4282 time to fit residues: 21.7334 Evaluate side-chains 35 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9399 ------------------------------------------------------------------------------- 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: 7.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.042961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.036721 restraints weight = 114489.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.038200 restraints weight = 56657.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.039268 restraints weight = 33476.077| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.6445 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= 0.125 Angle : 0.460 4.918 6286 Z= 0.232 Chirality : 0.038 0.141 716 Planarity : 0.004 0.035 802 Dihedral : 4.080 16.051 635 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.98 (0.38), residues: 532 helix: -0.45 (0.39), residues: 175 sheet: -0.66 (0.51), residues: 102 loop : -0.64 (0.44), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 455 HIS 0.003 0.001 HIS C 514 PHE 0.007 0.001 PHE C 826 TYR 0.010 0.001 TYR C 788 ARG 0.002 0.000 ARG C 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2288.17 seconds wall clock time: 41 minutes 15.72 seconds (2475.72 seconds total)