Starting phenix.real_space_refine on Wed Sep 25 17:09:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxe_30006/09_2024/6lxe_30006.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxe_30006/09_2024/6lxe_30006.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/6lxe_30006/09_2024/6lxe_30006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxe_30006/09_2024/6lxe_30006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxe_30006/09_2024/6lxe_30006.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxe_30006/09_2024/6lxe_30006.cif" } 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 Anisotropic ADP refinement not supported. Converting 5260 atoms to isotropic. 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 Zn 2 6.06 5 S 41 5.16 5 C 4145 2.51 5 N 1144 2.21 5 O 1187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6519 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 6133 Classifications: {'peptide': 768} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 41, 'TRANS': 726} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 205 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "C" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 179 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 868 SG CYS A 561 46.109 27.096 56.345 1.00175.10 S ATOM 1826 SG CYS A 676 43.492 29.089 55.869 1.00148.02 S ATOM 676 SG CYS A 536 30.126 51.769 48.423 1.00151.24 S ATOM 691 SG CYS A 538 29.902 54.514 44.875 1.00154.18 S Time building chain proxies: 3.81, per 1000 atoms: 0.58 Number of scatterers: 6519 At special positions: 0 Unit cell: (93.826, 117.828, 112.373, 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) Zn 2 29.99 S 41 16.00 O 1187 8.00 N 1144 7.00 C 4145 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 834.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 676 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 609 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 680 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 561 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 536 " pdb="ZN ZN A1402 " - pdb=" NE2 HIS A1026 " pdb="ZN ZN A1402 " - pdb=" NE2 HIS A 549 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 538 " Number of angles added : 4 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1556 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 49.0% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 438 through 452 removed outlier: 4.940A pdb=" N LYS A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 641 through 654 Processing helix chain 'A' and resid 698 through 709 Processing helix chain 'A' and resid 719 through 726 removed outlier: 4.292A pdb=" N GLU A 726 " --> pdb=" O MET A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 736 Processing helix chain 'A' and resid 790 through 804 Processing helix chain 'A' and resid 811 through 829 removed outlier: 4.114A pdb=" N LYS A 815 " --> pdb=" O LYS A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 861 removed outlier: 4.199A pdb=" N CYS A 857 " --> pdb=" O ARG A 853 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET A 861 " --> pdb=" O CYS A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 876 removed outlier: 4.439A pdb=" N VAL A 865 " --> pdb=" O MET A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 884 Processing helix chain 'A' and resid 890 through 897 removed outlier: 3.834A pdb=" N GLN A 894 " --> pdb=" O ARG A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 919 Processing helix chain 'A' and resid 965 through 988 removed outlier: 3.861A pdb=" N ALA A 974 " --> pdb=" O PHE A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1005 removed outlier: 3.515A pdb=" N GLN A1005 " --> pdb=" O THR A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1014 removed outlier: 3.757A pdb=" N LEU A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1055 removed outlier: 3.626A pdb=" N GLY A1055 " --> pdb=" O VAL A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1069 removed outlier: 3.724A pdb=" N ALA A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1080 Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1094 through 1098 Processing helix chain 'A' and resid 1104 through 1115 Processing helix chain 'A' and resid 1121 through 1128 Processing helix chain 'A' and resid 1145 through 1165 removed outlier: 3.817A pdb=" N LEU A1149 " --> pdb=" O ARG A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1180 Processing helix chain 'A' and resid 1183 through 1195 removed outlier: 4.255A pdb=" N GLN A1187 " --> pdb=" O ASN A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1232 Processing helix chain 'A' and resid 1233 through 1245 removed outlier: 3.954A pdb=" N VAL A1237 " --> pdb=" O ASP A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1255 removed outlier: 3.547A pdb=" N PHE A1252 " --> pdb=" O ARG A1248 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 750 Processing helix chain 'C' and resid 730 through 747 Processing sheet with id=AA1, first strand: chain 'A' and resid 413 through 415 removed outlier: 6.338A pdb=" N ARG A 414 " --> pdb=" O VAL A 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 619 through 621 removed outlier: 3.741A pdb=" N PHE A 604 " --> pdb=" O ILE A 576 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 740 through 742 278 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2181 1.34 - 1.46: 1457 1.46 - 1.58: 2966 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 6669 Sorted by residual: bond pdb=" C VAL A 714 " pdb=" N PRO A 715 " ideal model delta sigma weight residual 1.334 1.349 -0.015 1.11e-02 8.12e+03 1.94e+00 bond pdb=" C THR A 898 " pdb=" N HIS A 899 " ideal model delta sigma weight residual 1.331 1.306 0.025 2.07e-02 2.33e+03 1.40e+00 bond pdb=" CB PRO A 581 " pdb=" CG PRO A 581 " ideal model delta sigma weight residual 1.492 1.533 -0.041 5.00e-02 4.00e+02 6.81e-01 bond pdb=" CA ILE A 767 " pdb=" CB ILE A 767 " ideal model delta sigma weight residual 1.540 1.532 0.008 1.01e-02 9.80e+03 6.30e-01 bond pdb=" N ALA A 712 " pdb=" CA ALA A 712 " ideal model delta sigma weight residual 1.457 1.468 -0.010 1.29e-02 6.01e+03 6.30e-01 ... (remaining 6664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 8708 1.39 - 2.78: 260 2.78 - 4.17: 40 4.17 - 5.56: 19 5.56 - 6.95: 2 Bond angle restraints: 9029 Sorted by residual: angle pdb=" C ARG A 562 " pdb=" N PRO A 563 " pdb=" CA PRO A 563 " ideal model delta sigma weight residual 118.85 122.90 -4.05 1.09e+00 8.42e-01 1.38e+01 angle pdb=" N CYS A 536 " pdb=" CA CYS A 536 " pdb=" C CYS A 536 " ideal model delta sigma weight residual 108.20 113.11 -4.91 1.71e+00 3.42e-01 8.25e+00 angle pdb=" C LYS A 559 " pdb=" N PRO A 560 " pdb=" CA PRO A 560 " ideal model delta sigma weight residual 119.84 122.83 -2.99 1.25e+00 6.40e-01 5.71e+00 angle pdb=" C HIS A 630 " pdb=" N PHE A 631 " pdb=" CA PHE A 631 " ideal model delta sigma weight residual 121.54 126.00 -4.46 1.91e+00 2.74e-01 5.45e+00 angle pdb=" CA LEU C 735 " pdb=" CB LEU C 735 " pdb=" CG LEU C 735 " ideal model delta sigma weight residual 116.30 123.25 -6.95 3.50e+00 8.16e-02 3.94e+00 ... (remaining 9024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3600 17.92 - 35.84: 347 35.84 - 53.76: 63 53.76 - 71.68: 13 71.68 - 89.60: 9 Dihedral angle restraints: 4032 sinusoidal: 1643 harmonic: 2389 Sorted by residual: dihedral pdb=" CA PRO A 779 " pdb=" C PRO A 779 " pdb=" N ALA A 780 " pdb=" CA ALA A 780 " ideal model delta harmonic sigma weight residual -180.00 -157.89 -22.11 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA TRP A 848 " pdb=" C TRP A 848 " pdb=" N LYS A 849 " pdb=" CA LYS A 849 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PHE A 631 " pdb=" C PHE A 631 " pdb=" N ILE A 632 " pdb=" CA ILE A 632 " ideal model delta harmonic sigma weight residual 180.00 -163.99 -16.01 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 4029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 500 0.024 - 0.047: 289 0.047 - 0.071: 128 0.071 - 0.094: 50 0.094 - 0.118: 25 Chirality restraints: 992 Sorted by residual: chirality pdb=" CA ILE A 576 " pdb=" N ILE A 576 " pdb=" C ILE A 576 " pdb=" CB ILE A 576 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.46e-01 chirality pdb=" CA ILE A 592 " pdb=" N ILE A 592 " pdb=" C ILE A 592 " pdb=" CB ILE A 592 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA VAL A 742 " pdb=" N VAL A 742 " pdb=" C VAL A 742 " pdb=" CB VAL A 742 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.26e-01 ... (remaining 989 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 580 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A 581 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 581 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 581 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 579 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 580 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 580 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 580 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 579 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.26e+00 pdb=" C SER A 579 " -0.019 2.00e-02 2.50e+03 pdb=" O SER A 579 " 0.007 2.00e-02 2.50e+03 pdb=" N PRO A 580 " 0.007 2.00e-02 2.50e+03 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 72 2.60 - 3.18: 5710 3.18 - 3.75: 10902 3.75 - 4.33: 13621 4.33 - 4.90: 21403 Nonbonded interactions: 51708 Sorted by model distance: nonbonded pdb=" OG SER A 433 " pdb=" CG2 THR A 565 " model vdw 2.030 3.460 nonbonded pdb=" O ARG A1213 " pdb=" OG1 THR A1216 " model vdw 2.201 3.040 nonbonded pdb=" O ARG A 914 " pdb=" OG SER A 918 " model vdw 2.225 3.040 nonbonded pdb=" O GLN A1096 " pdb=" OG1 THR A1100 " model vdw 2.245 3.040 nonbonded pdb=" N GLY A 739 " pdb=" O ILE A 754 " model vdw 2.253 3.120 ... (remaining 51703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 729 through 749) selection = chain 'C' } 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.030 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 : 0.002 0.041 6669 Z= 0.154 Angle : 0.588 6.952 9029 Z= 0.329 Chirality : 0.038 0.118 992 Planarity : 0.003 0.043 1177 Dihedral : 15.295 89.603 2476 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 0.14 % Allowed : 7.06 % Favored : 92.80 % 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: -3.22 (0.27), residues: 803 helix: -0.83 (0.25), residues: 367 sheet: -1.64 (0.87), residues: 39 loop : -3.62 (0.27), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 848 HIS 0.004 0.001 HIS A 983 PHE 0.008 0.001 PHE A 970 TYR 0.006 0.001 TYR A1229 ARG 0.002 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 0.793 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: A 861 MET cc_start: 0.7725 (mtm) cc_final: 0.7288 (mtt) REVERT: A 872 TYR cc_start: 0.8182 (t80) cc_final: 0.7952 (t80) REVERT: A 914 ARG cc_start: 0.8821 (ttm110) cc_final: 0.8080 (tpt170) REVERT: A 1011 MET cc_start: 0.9073 (ptm) cc_final: 0.8745 (ppp) REVERT: A 1021 PHE cc_start: 0.8098 (m-80) cc_final: 0.7806 (m-80) REVERT: A 1241 MET cc_start: 0.8061 (mmp) cc_final: 0.7487 (tpp) outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.1982 time to fit residues: 39.0117 Evaluate side-chains 101 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 0.1980 chunk 46 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN A 531 ASN A 630 HIS ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 GLN A 724 GLN A 858 GLN A 868 HIS A 909 ASN A 915 ASN A 924 GLN A1038 HIS ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1144 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6669 Z= 0.185 Angle : 0.617 8.002 9029 Z= 0.306 Chirality : 0.041 0.133 992 Planarity : 0.005 0.055 1177 Dihedral : 4.278 22.310 884 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.14 % Allowed : 5.33 % Favored : 94.52 % 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: -2.41 (0.29), residues: 803 helix: 0.01 (0.27), residues: 370 sheet: -1.43 (0.86), residues: 39 loop : -3.38 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 848 HIS 0.011 0.001 HIS A 630 PHE 0.029 0.001 PHE A1224 TYR 0.010 0.001 TYR A 574 ARG 0.005 0.001 ARG A1178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 0.816 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: A 636 MET cc_start: 0.7959 (ppp) cc_final: 0.7719 (ppp) REVERT: A 861 MET cc_start: 0.7740 (mtm) cc_final: 0.7033 (tmm) REVERT: A 914 ARG cc_start: 0.8892 (ttm110) cc_final: 0.8304 (tpt170) REVERT: A 966 GLU cc_start: 0.7376 (pt0) cc_final: 0.7082 (pt0) REVERT: A 1155 GLN cc_start: 0.5972 (mm110) cc_final: 0.5282 (tp40) REVERT: A 1241 MET cc_start: 0.8052 (mmp) cc_final: 0.7620 (tpt) REVERT: B 737 GLU cc_start: 0.9328 (mp0) cc_final: 0.8964 (mp0) REVERT: B 739 MET cc_start: 0.8690 (mmp) cc_final: 0.8371 (mmt) REVERT: C 739 MET cc_start: 0.6998 (tpt) cc_final: 0.6088 (tmm) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1758 time to fit residues: 31.2699 Evaluate side-chains 103 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 60 optimal weight: 0.0470 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 overall best weight: 5.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 HIS ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 GLN ** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 ASN ** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6669 Z= 0.342 Angle : 0.773 9.347 9029 Z= 0.393 Chirality : 0.045 0.130 992 Planarity : 0.006 0.055 1177 Dihedral : 5.116 27.184 884 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 24.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.14 % Allowed : 9.08 % Favored : 90.78 % 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: -2.75 (0.28), residues: 803 helix: -0.50 (0.26), residues: 382 sheet: -1.57 (0.85), residues: 39 loop : -3.39 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 848 HIS 0.010 0.002 HIS A 630 PHE 0.019 0.003 PHE A 572 TYR 0.028 0.003 TYR A1229 ARG 0.006 0.001 ARG A1178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 0.706 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: A 530 MET cc_start: 0.7864 (tmm) cc_final: 0.7541 (tmm) REVERT: A 606 MET cc_start: 0.7933 (mtp) cc_final: 0.7665 (mtp) REVERT: A 699 MET cc_start: 0.8735 (mmm) cc_final: 0.8355 (mmm) REVERT: A 914 ARG cc_start: 0.8944 (ttm110) cc_final: 0.8261 (tpt170) REVERT: A 1155 GLN cc_start: 0.5423 (mm110) cc_final: 0.4728 (mm110) REVERT: B 739 MET cc_start: 0.8755 (mmp) cc_final: 0.8275 (mmt) REVERT: B 748 GLU cc_start: 0.8311 (pt0) cc_final: 0.7861 (pp20) REVERT: C 730 HIS cc_start: 0.9383 (p-80) cc_final: 0.9047 (p-80) REVERT: C 739 MET cc_start: 0.7359 (tpt) cc_final: 0.7114 (tpt) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.1655 time to fit residues: 26.6093 Evaluate side-chains 85 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 ASN ** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 HIS A1222 GLN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6669 Z= 0.272 Angle : 0.712 9.981 9029 Z= 0.358 Chirality : 0.044 0.126 992 Planarity : 0.005 0.061 1177 Dihedral : 5.139 25.256 884 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % 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: -2.56 (0.28), residues: 803 helix: -0.29 (0.26), residues: 376 sheet: -1.71 (0.81), residues: 39 loop : -3.28 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1078 HIS 0.009 0.002 HIS A 630 PHE 0.034 0.002 PHE A1224 TYR 0.022 0.002 TYR A1229 ARG 0.007 0.001 ARG A1178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.795 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: A 606 MET cc_start: 0.8061 (mtp) cc_final: 0.7693 (mtp) REVERT: A 699 MET cc_start: 0.8775 (mmm) cc_final: 0.8506 (mmm) REVERT: A 899 HIS cc_start: 0.7913 (t-170) cc_final: 0.7577 (t-170) REVERT: A 914 ARG cc_start: 0.8910 (ttm110) cc_final: 0.8244 (tpt170) REVERT: A 1021 PHE cc_start: 0.7821 (m-80) cc_final: 0.7589 (m-10) REVERT: A 1155 GLN cc_start: 0.5537 (mm110) cc_final: 0.5219 (tp-100) REVERT: A 1241 MET cc_start: 0.8670 (mmp) cc_final: 0.8170 (tpt) REVERT: B 739 MET cc_start: 0.8642 (mmp) cc_final: 0.8180 (mmt) REVERT: B 748 GLU cc_start: 0.8122 (pt0) cc_final: 0.7727 (pp20) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1848 time to fit residues: 30.2553 Evaluate side-chains 87 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 ASN ** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN ** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 ASN ** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 HIS A1155 GLN A1173 HIS A1256 GLN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6669 Z= 0.342 Angle : 0.805 13.009 9029 Z= 0.413 Chirality : 0.047 0.146 992 Planarity : 0.006 0.064 1177 Dihedral : 5.669 26.857 884 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 27.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 0.14 % Allowed : 5.76 % Favored : 94.09 % 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: -2.77 (0.28), residues: 803 helix: -0.61 (0.26), residues: 372 sheet: -1.57 (0.85), residues: 35 loop : -3.21 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 662 HIS 0.011 0.002 HIS A 630 PHE 0.023 0.003 PHE A1224 TYR 0.027 0.003 TYR A1081 ARG 0.009 0.001 ARG A1178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.735 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: A 530 MET cc_start: 0.7985 (tmm) cc_final: 0.7501 (tmm) REVERT: A 606 MET cc_start: 0.8085 (mtp) cc_final: 0.7843 (mtp) REVERT: A 628 THR cc_start: 0.8713 (p) cc_final: 0.8510 (p) REVERT: A 660 TYR cc_start: 0.7488 (t80) cc_final: 0.6483 (t80) REVERT: A 699 MET cc_start: 0.8789 (mmm) cc_final: 0.8493 (mmm) REVERT: A 891 CYS cc_start: 0.8758 (t) cc_final: 0.8527 (m) REVERT: A 914 ARG cc_start: 0.8930 (ttm110) cc_final: 0.8011 (tpt170) REVERT: A 917 LEU cc_start: 0.9062 (mt) cc_final: 0.8803 (pp) REVERT: A 1155 GLN cc_start: 0.6890 (tp-100) cc_final: 0.6675 (mm-40) REVERT: A 1236 TYR cc_start: 0.7744 (t80) cc_final: 0.6989 (t80) REVERT: A 1241 MET cc_start: 0.8729 (mmp) cc_final: 0.7918 (tpt) REVERT: B 739 MET cc_start: 0.8567 (mmp) cc_final: 0.8221 (mmt) REVERT: C 739 MET cc_start: 0.7048 (tpt) cc_final: 0.5830 (tmm) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1960 time to fit residues: 28.2999 Evaluate side-chains 84 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.0670 chunk 15 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 HIS ** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN ** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 ASN A1045 GLN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6669 Z= 0.254 Angle : 0.724 11.647 9029 Z= 0.367 Chirality : 0.044 0.138 992 Planarity : 0.005 0.061 1177 Dihedral : 5.456 26.301 884 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % 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: -2.54 (0.29), residues: 803 helix: -0.24 (0.27), residues: 376 sheet: -2.04 (0.80), residues: 39 loop : -3.26 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1078 HIS 0.007 0.001 HIS A 983 PHE 0.018 0.002 PHE A 679 TYR 0.019 0.002 TYR A1229 ARG 0.006 0.000 ARG A1178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.755 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: A 530 MET cc_start: 0.7786 (tmm) cc_final: 0.7386 (tmm) REVERT: A 564 MET cc_start: 0.6525 (mmt) cc_final: 0.6069 (mmt) REVERT: A 699 MET cc_start: 0.8729 (mmm) cc_final: 0.8458 (mmm) REVERT: A 914 ARG cc_start: 0.8895 (ttm110) cc_final: 0.8042 (tpt170) REVERT: A 1155 GLN cc_start: 0.6848 (tp-100) cc_final: 0.6451 (mm110) REVERT: A 1241 MET cc_start: 0.8736 (mmp) cc_final: 0.8191 (tpt) REVERT: A 1242 ASN cc_start: 0.8621 (t0) cc_final: 0.7793 (p0) REVERT: B 739 MET cc_start: 0.8477 (mmp) cc_final: 0.8273 (mmt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1968 time to fit residues: 29.7357 Evaluate side-chains 87 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 HIS ** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN ** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6669 Z= 0.226 Angle : 0.712 10.279 9029 Z= 0.359 Chirality : 0.044 0.125 992 Planarity : 0.005 0.070 1177 Dihedral : 5.353 25.318 884 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: -2.43 (0.29), residues: 803 helix: -0.14 (0.27), residues: 378 sheet: -1.72 (0.81), residues: 39 loop : -3.27 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1078 HIS 0.007 0.001 HIS A 983 PHE 0.029 0.002 PHE A 631 TYR 0.018 0.002 TYR A1229 ARG 0.005 0.001 ARG A1178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.7756 (tmm) cc_final: 0.7410 (tmm) REVERT: A 606 MET cc_start: 0.8082 (mtp) cc_final: 0.7794 (mtp) REVERT: A 699 MET cc_start: 0.8824 (mmm) cc_final: 0.8567 (mmm) REVERT: A 914 ARG cc_start: 0.8931 (ttm110) cc_final: 0.8318 (tpt170) REVERT: A 1155 GLN cc_start: 0.6963 (tp-100) cc_final: 0.6596 (mm110) REVERT: A 1236 TYR cc_start: 0.7709 (t80) cc_final: 0.7127 (t80) REVERT: A 1241 MET cc_start: 0.8655 (mmp) cc_final: 0.8128 (tpt) REVERT: A 1242 ASN cc_start: 0.8454 (t0) cc_final: 0.7735 (p0) REVERT: B 737 GLU cc_start: 0.9164 (mp0) cc_final: 0.8911 (mp0) REVERT: C 739 MET cc_start: 0.6940 (tpt) cc_final: 0.5768 (tmm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1974 time to fit residues: 29.1082 Evaluate side-chains 84 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 60 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS ** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN A 915 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6669 Z= 0.191 Angle : 0.723 9.235 9029 Z= 0.357 Chirality : 0.043 0.151 992 Planarity : 0.005 0.065 1177 Dihedral : 5.126 27.211 884 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: -2.19 (0.29), residues: 803 helix: 0.09 (0.27), residues: 380 sheet: -1.23 (0.85), residues: 39 loop : -3.23 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 662 HIS 0.007 0.001 HIS A 983 PHE 0.015 0.001 PHE A1224 TYR 0.012 0.001 TYR A 552 ARG 0.007 0.001 ARG C 746 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.7726 (tmm) cc_final: 0.7244 (tmm) REVERT: A 888 GLN cc_start: 0.8673 (tp40) cc_final: 0.8334 (tp-100) REVERT: A 914 ARG cc_start: 0.8966 (ttm110) cc_final: 0.8365 (tpt170) REVERT: A 1058 GLU cc_start: 0.8337 (pm20) cc_final: 0.7677 (tm-30) REVERT: A 1155 GLN cc_start: 0.6943 (tp-100) cc_final: 0.6544 (mm110) REVERT: A 1236 TYR cc_start: 0.7523 (t80) cc_final: 0.7037 (t80) REVERT: A 1241 MET cc_start: 0.8442 (mmp) cc_final: 0.7966 (tpt) REVERT: A 1242 ASN cc_start: 0.8206 (t0) cc_final: 0.7675 (p0) REVERT: B 737 GLU cc_start: 0.9131 (mp0) cc_final: 0.8787 (mp0) REVERT: C 739 MET cc_start: 0.7087 (tpt) cc_final: 0.6164 (tmm) REVERT: C 747 GLU cc_start: 0.6999 (pt0) cc_final: 0.6771 (pt0) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1712 time to fit residues: 27.6091 Evaluate side-chains 88 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 0.0370 chunk 67 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 HIS A 915 ASN A 964 HIS ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 HIS A1256 GLN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6669 Z= 0.191 Angle : 0.711 9.584 9029 Z= 0.355 Chirality : 0.043 0.160 992 Planarity : 0.005 0.058 1177 Dihedral : 5.053 23.675 884 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 0.14 % Allowed : 0.58 % Favored : 99.28 % 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: -2.17 (0.29), residues: 803 helix: 0.11 (0.27), residues: 379 sheet: -1.25 (0.84), residues: 39 loop : -3.22 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1078 HIS 0.006 0.001 HIS A 983 PHE 0.030 0.002 PHE A 631 TYR 0.016 0.001 TYR A1229 ARG 0.006 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.772 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: A 530 MET cc_start: 0.7753 (tmm) cc_final: 0.7255 (tmm) REVERT: A 682 MET cc_start: 0.7541 (ttm) cc_final: 0.6902 (ttm) REVERT: A 888 GLN cc_start: 0.8679 (tp40) cc_final: 0.8355 (tp-100) REVERT: A 914 ARG cc_start: 0.8946 (ttm110) cc_final: 0.8154 (tpt170) REVERT: A 1058 GLU cc_start: 0.8325 (pm20) cc_final: 0.7620 (tm-30) REVERT: A 1155 GLN cc_start: 0.6952 (tp-100) cc_final: 0.6586 (mm110) REVERT: A 1241 MET cc_start: 0.8534 (mmp) cc_final: 0.8126 (tpt) REVERT: C 730 HIS cc_start: 0.9406 (p-80) cc_final: 0.9203 (p-80) outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.1638 time to fit residues: 25.6303 Evaluate side-chains 90 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 67 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 HIS A 915 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6669 Z= 0.212 Angle : 0.718 9.845 9029 Z= 0.362 Chirality : 0.043 0.136 992 Planarity : 0.005 0.061 1177 Dihedral : 5.083 23.794 884 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -2.18 (0.29), residues: 803 helix: 0.11 (0.27), residues: 380 sheet: -1.34 (0.80), residues: 39 loop : -3.22 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1078 HIS 0.007 0.001 HIS A 983 PHE 0.028 0.002 PHE A 631 TYR 0.019 0.002 TYR A1229 ARG 0.007 0.000 ARG A 753 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 MET cc_start: 0.8234 (mtp) cc_final: 0.7899 (mtp) REVERT: A 660 TYR cc_start: 0.7210 (t80) cc_final: 0.6737 (t80) REVERT: A 861 MET cc_start: 0.8022 (mmt) cc_final: 0.7576 (tmm) REVERT: A 888 GLN cc_start: 0.8699 (tp40) cc_final: 0.8386 (tp-100) REVERT: A 914 ARG cc_start: 0.8925 (ttm110) cc_final: 0.8359 (tpt170) REVERT: A 1155 GLN cc_start: 0.6957 (tp-100) cc_final: 0.6574 (mm110) REVERT: A 1241 MET cc_start: 0.8511 (mmp) cc_final: 0.8118 (tpt) REVERT: B 737 GLU cc_start: 0.9158 (mp0) cc_final: 0.8803 (mp0) REVERT: C 739 MET cc_start: 0.7254 (tpt) cc_final: 0.5824 (tmm) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1631 time to fit residues: 25.0706 Evaluate side-chains 80 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 0.0670 chunk 63 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 0.0970 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 overall best weight: 0.8118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.088195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.075885 restraints weight = 41650.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.077140 restraints weight = 31832.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.078085 restraints weight = 25770.987| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6669 Z= 0.181 Angle : 0.713 9.554 9029 Z= 0.349 Chirality : 0.043 0.167 992 Planarity : 0.004 0.057 1177 Dihedral : 4.900 23.425 884 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -2.07 (0.29), residues: 803 helix: 0.22 (0.27), residues: 380 sheet: -1.36 (0.83), residues: 38 loop : -3.18 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1078 HIS 0.007 0.001 HIS A 983 PHE 0.029 0.001 PHE A 631 TYR 0.012 0.001 TYR A 552 ARG 0.004 0.000 ARG A 753 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1452.97 seconds wall clock time: 26 minutes 40.88 seconds (1600.88 seconds total)