Starting phenix.real_space_refine on Thu Feb 13 04:28:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w64_21552/02_2025/6w64_21552.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w64_21552/02_2025/6w64_21552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w64_21552/02_2025/6w64_21552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w64_21552/02_2025/6w64_21552.map" model { file = "/net/cci-nas-00/data/ceres_data/6w64_21552/02_2025/6w64_21552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w64_21552/02_2025/6w64_21552.cif" } resolution = 3.9 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 P 56 5.49 5 S 34 5.16 5 C 5213 2.51 5 N 1474 2.21 5 O 1728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8505 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7331 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 32, 'TRANS': 895} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 805 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 13, 'rna3p_pyr': 14} Link IDs: {'rna2p': 11, 'rna3p': 26} Chain: "C" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 369 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Time building chain proxies: 5.70, per 1000 atoms: 0.67 Number of scatterers: 8505 At special positions: 0 Unit cell: (85.05, 128.1, 108.15, 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 34 16.00 P 56 15.00 O 1728 8.00 N 1474 7.00 C 5213 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: 3.17 Conformation dependent library (CDL) restraints added in 900.7 milliseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 55.7% alpha, 7.2% beta 13 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 23 through 54 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.630A pdb=" N LEU A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 282 through 293 Processing helix chain 'A' and resid 297 through 332 Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 371 through 393 removed outlier: 4.539A pdb=" N THR A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 422 Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 444 through 463 Processing helix chain 'A' and resid 490 through 501 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 708 through 721 removed outlier: 3.804A pdb=" N LYS A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 747 removed outlier: 3.531A pdb=" N ILE A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 771 Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.569A pdb=" N ALA A 775 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS A 776 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 787 Processing helix chain 'A' and resid 800 through 822 Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 846 through 886 Processing helix chain 'A' and resid 905 through 914 removed outlier: 3.638A pdb=" N ASP A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 929 Processing helix chain 'A' and resid 967 through 971 Processing helix chain 'A' and resid 972 through 984 Processing helix chain 'A' and resid 990 through 1008 Processing helix chain 'A' and resid 1010 through 1015 Processing helix chain 'A' and resid 1018 through 1033 Processing helix chain 'A' and resid 1072 through 1082 Processing helix chain 'A' and resid 1085 through 1090 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 7.423A pdb=" N ASN A 477 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY A 486 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY A 479 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE A 488 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU A 485 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A 523 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA A 530 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84 removed outlier: 3.595A pdb=" N LYS A 81 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 678 through 683 removed outlier: 6.268A pdb=" N GLU A 660 " --> pdb=" O PRO A 678 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 680 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 669 through 670 Processing sheet with id=AA5, first strand: chain 'A' and resid 687 through 689 Processing sheet with id=AA6, first strand: chain 'A' and resid 893 through 894 removed outlier: 7.012A pdb=" N GLY A 893 " --> pdb=" O VAL A 939 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1049 through 1050 406 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1268 1.28 - 1.41: 2320 1.41 - 1.54: 5026 1.54 - 1.68: 118 1.68 - 1.81: 58 Bond restraints: 8790 Sorted by residual: bond pdb=" C PHE A 80 " pdb=" O PHE A 80 " ideal model delta sigma weight residual 1.233 1.148 0.084 1.12e-02 7.97e+03 5.68e+01 bond pdb=" N ARG A 962 " pdb=" CA ARG A 962 " ideal model delta sigma weight residual 1.454 1.493 -0.038 1.17e-02 7.31e+03 1.07e+01 bond pdb=" N LYS A 81 " pdb=" CA LYS A 81 " ideal model delta sigma weight residual 1.454 1.493 -0.040 1.23e-02 6.61e+03 1.03e+01 bond pdb=" C ASN A1064 " pdb=" N GLY A1065 " ideal model delta sigma weight residual 1.331 1.376 -0.046 1.46e-02 4.69e+03 9.74e+00 bond pdb=" N GLY A 682 " pdb=" CA GLY A 682 " ideal model delta sigma weight residual 1.448 1.480 -0.031 1.00e-02 1.00e+04 9.62e+00 ... (remaining 8785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 11873 1.75 - 3.50: 193 3.50 - 5.25: 38 5.25 - 6.99: 2 6.99 - 8.74: 3 Bond angle restraints: 12109 Sorted by residual: angle pdb=" N PRO A 987 " pdb=" CA PRO A 987 " pdb=" CB PRO A 987 " ideal model delta sigma weight residual 103.36 110.25 -6.89 8.80e-01 1.29e+00 6.14e+01 angle pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" O PHE A 80 " ideal model delta sigma weight residual 120.89 112.15 8.74 1.27e+00 6.20e-01 4.74e+01 angle pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" N LYS A 81 " ideal model delta sigma weight residual 115.75 123.12 -7.37 1.08e+00 8.57e-01 4.66e+01 angle pdb=" C ASN A1064 " pdb=" N GLY A1065 " pdb=" CA GLY A1065 " ideal model delta sigma weight residual 121.41 129.72 -8.31 1.96e+00 2.60e-01 1.80e+01 angle pdb=" O SER A 95 " pdb=" C SER A 95 " pdb=" N ASN A 96 " ideal model delta sigma weight residual 122.07 125.89 -3.82 1.03e+00 9.43e-01 1.37e+01 ... (remaining 12104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 5153 34.97 - 69.93: 195 69.93 - 104.90: 17 104.90 - 139.86: 0 139.86 - 174.83: 3 Dihedral angle restraints: 5368 sinusoidal: 2635 harmonic: 2733 Sorted by residual: dihedral pdb=" O4' U B 11 " pdb=" C1' U B 11 " pdb=" N1 U B 11 " pdb=" C2 U B 11 " ideal model delta sinusoidal sigma weight residual -160.00 -7.34 -152.66 1 1.50e+01 4.44e-03 8.06e+01 dihedral pdb=" O4' U B -6 " pdb=" C1' U B -6 " pdb=" N1 U B -6 " pdb=" C2 U B -6 " ideal model delta sinusoidal sigma weight residual -128.00 46.83 -174.83 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA LYS A 487 " pdb=" C LYS A 487 " pdb=" N ILE A 488 " pdb=" CA ILE A 488 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 5365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1077 0.038 - 0.076: 212 0.076 - 0.114: 61 0.114 - 0.153: 13 0.153 - 0.191: 4 Chirality restraints: 1367 Sorted by residual: chirality pdb=" C2' A B -10 " pdb=" C3' A B -10 " pdb=" O2' A B -10 " pdb=" C1' A B -10 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CA PRO A 987 " pdb=" N PRO A 987 " pdb=" C PRO A 987 " pdb=" CB PRO A 987 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" C3' C B -8 " pdb=" C4' C B -8 " pdb=" O3' C B -8 " pdb=" C2' C B -8 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.18 2.00e-01 2.50e+01 8.15e-01 ... (remaining 1364 not shown) Planarity restraints: 1338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 681 " -0.017 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C SER A 681 " 0.055 2.00e-02 2.50e+03 pdb=" O SER A 681 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY A 682 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 80 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C PHE A 80 " 0.036 2.00e-02 2.50e+03 pdb=" O PHE A 80 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 81 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 96 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C ASN A 96 " 0.031 2.00e-02 2.50e+03 pdb=" O ASN A 96 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 97 " -0.011 2.00e-02 2.50e+03 ... (remaining 1335 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 830 2.74 - 3.28: 8889 3.28 - 3.82: 14483 3.82 - 4.36: 16738 4.36 - 4.90: 28352 Nonbonded interactions: 69292 Sorted by model distance: nonbonded pdb=" NH2 ARG A 57 " pdb=" OD1 ASP A 72 " model vdw 2.196 3.120 nonbonded pdb=" O SER A 981 " pdb=" OG SER A 984 " model vdw 2.203 3.040 nonbonded pdb=" NH1 ARG A 853 " pdb=" OE2 GLU A 857 " model vdw 2.206 3.120 nonbonded pdb=" O ASN A 96 " pdb=" ND2 ASN A 96 " model vdw 2.207 3.120 nonbonded pdb=" O TYR A 104 " pdb=" OG SER A 105 " model vdw 2.216 3.040 ... (remaining 69287 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 ========== 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.820 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8790 Z= 0.201 Angle : 0.577 8.742 12109 Z= 0.371 Chirality : 0.037 0.191 1367 Planarity : 0.003 0.032 1338 Dihedral : 16.240 174.826 3600 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.99 % Favored : 92.90 % Rotamer: Outliers : 1.29 % Allowed : 3.10 % Favored : 95.60 % 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: 0.30 (0.29), residues: 916 helix: 2.21 (0.24), residues: 501 sheet: -2.20 (0.54), residues: 74 loop : -2.47 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 79 HIS 0.004 0.001 HIS A 952 PHE 0.007 0.001 PHE A 911 TYR 0.024 0.001 TYR A 695 ARG 0.002 0.000 ARG A 918 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 248 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 PRO cc_start: 0.8928 (Cg_endo) cc_final: 0.8658 (Cg_exo) REVERT: A 539 GLU cc_start: 0.4956 (tp30) cc_final: 0.3804 (tp30) REVERT: A 806 MET cc_start: 0.7081 (ttp) cc_final: 0.6849 (ttp) REVERT: A 850 PHE cc_start: 0.8922 (t80) cc_final: 0.8485 (t80) REVERT: A 918 ARG cc_start: 0.6123 (mmm-85) cc_final: 0.5808 (mmm-85) REVERT: A 929 MET cc_start: 0.7473 (mtt) cc_final: 0.7213 (mtp) REVERT: A 940 ASN cc_start: 0.7558 (t0) cc_final: 0.6848 (p0) REVERT: A 1074 ASP cc_start: 0.6322 (p0) cc_final: 0.5873 (p0) outliers start: 10 outliers final: 4 residues processed: 256 average time/residue: 0.2493 time to fit residues: 83.8386 Evaluate side-chains 144 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 890 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 HIS A 471 GLN A 616 ASN A 672 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.140847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.114135 restraints weight = 18670.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.115818 restraints weight = 16536.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.116460 restraints weight = 11019.254| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 8790 Z= 0.436 Angle : 0.811 12.224 12109 Z= 0.423 Chirality : 0.047 0.168 1367 Planarity : 0.005 0.043 1338 Dihedral : 19.970 179.724 1816 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 3.10 % Allowed : 12.55 % Favored : 84.35 % 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: -0.67 (0.28), residues: 916 helix: 1.27 (0.23), residues: 513 sheet: -2.85 (0.49), residues: 89 loop : -2.67 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 915 HIS 0.009 0.002 HIS A 24 PHE 0.023 0.003 PHE A 743 TYR 0.029 0.003 TYR A 406 ARG 0.006 0.001 ARG A1043 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.815 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 19 MET cc_start: 0.6331 (tpt) cc_final: 0.5920 (tpt) REVERT: A 159 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7047 (tp30) REVERT: A 539 GLU cc_start: 0.4815 (tp30) cc_final: 0.3520 (tp30) REVERT: A 918 ARG cc_start: 0.6987 (mmm-85) cc_final: 0.6739 (mmm-85) REVERT: A 940 ASN cc_start: 0.8053 (t0) cc_final: 0.7394 (p0) REVERT: A 948 ASP cc_start: 0.7450 (t0) cc_final: 0.7232 (t0) outliers start: 24 outliers final: 16 residues processed: 159 average time/residue: 0.2070 time to fit residues: 45.4980 Evaluate side-chains 130 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 951 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 34 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 31 optimal weight: 0.3980 chunk 85 optimal weight: 30.0000 chunk 23 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.144517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.117015 restraints weight = 18859.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.116668 restraints weight = 14185.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.117860 restraints weight = 11684.999| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8790 Z= 0.221 Angle : 0.643 12.241 12109 Z= 0.333 Chirality : 0.041 0.162 1367 Planarity : 0.004 0.069 1338 Dihedral : 19.919 177.530 1811 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.85 % Allowed : 14.75 % Favored : 82.41 % 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: -0.37 (0.28), residues: 916 helix: 1.69 (0.23), residues: 499 sheet: -2.72 (0.48), residues: 97 loop : -2.69 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 915 HIS 0.003 0.001 HIS A 527 PHE 0.039 0.002 PHE A 80 TYR 0.024 0.002 TYR A 406 ARG 0.005 0.001 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6123 (tpt) cc_final: 0.5778 (tpt) REVERT: A 116 TYR cc_start: 0.8444 (t80) cc_final: 0.8242 (t80) REVERT: A 159 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6848 (tp30) REVERT: A 940 ASN cc_start: 0.8078 (t0) cc_final: 0.7479 (p0) outliers start: 22 outliers final: 13 residues processed: 159 average time/residue: 0.2150 time to fit residues: 48.1277 Evaluate side-chains 136 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 951 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 91 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 477 ASN A 616 ASN A 711 HIS A 895 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.143585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.115921 restraints weight = 18669.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.115800 restraints weight = 14332.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.117678 restraints weight = 10950.326| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8790 Z= 0.237 Angle : 0.637 12.934 12109 Z= 0.330 Chirality : 0.042 0.160 1367 Planarity : 0.004 0.032 1338 Dihedral : 19.952 179.139 1811 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 2.46 % Allowed : 16.17 % Favored : 81.37 % 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: -0.38 (0.28), residues: 916 helix: 1.67 (0.23), residues: 499 sheet: -2.62 (0.49), residues: 95 loop : -2.71 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 915 HIS 0.004 0.001 HIS A 952 PHE 0.024 0.002 PHE A 743 TYR 0.019 0.002 TYR A 406 ARG 0.003 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6171 (tpt) cc_final: 0.5836 (tpt) REVERT: A 116 TYR cc_start: 0.8447 (t80) cc_final: 0.8163 (t80) REVERT: A 159 GLU cc_start: 0.7284 (mm-30) cc_final: 0.7070 (tp30) REVERT: A 476 PHE cc_start: 0.7374 (m-80) cc_final: 0.7160 (m-80) REVERT: A 539 GLU cc_start: 0.4710 (tp30) cc_final: 0.3500 (tp30) REVERT: A 940 ASN cc_start: 0.8078 (t0) cc_final: 0.7419 (p0) REVERT: A 948 ASP cc_start: 0.7374 (t0) cc_final: 0.7071 (t0) REVERT: A 1043 ARG cc_start: 0.6492 (mmt180) cc_final: 0.5794 (tpp80) outliers start: 19 outliers final: 13 residues processed: 149 average time/residue: 0.1850 time to fit residues: 39.1397 Evaluate side-chains 139 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 951 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 50.0000 chunk 88 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 46 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 4 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.147071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.119745 restraints weight = 18441.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.121876 restraints weight = 13428.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.122968 restraints weight = 9455.188| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8790 Z= 0.164 Angle : 0.603 12.705 12109 Z= 0.309 Chirality : 0.040 0.187 1367 Planarity : 0.003 0.030 1338 Dihedral : 19.861 178.111 1811 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.59 % Allowed : 17.08 % Favored : 80.34 % 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: -0.19 (0.28), residues: 916 helix: 1.74 (0.23), residues: 504 sheet: -2.52 (0.47), residues: 95 loop : -2.55 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 915 HIS 0.002 0.000 HIS A 528 PHE 0.037 0.002 PHE A 80 TYR 0.018 0.001 TYR A 301 ARG 0.003 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6210 (tpt) cc_final: 0.5918 (tpt) REVERT: A 116 TYR cc_start: 0.8279 (t80) cc_final: 0.7997 (t80) REVERT: A 159 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6872 (tp30) REVERT: A 537 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6979 (mm) REVERT: A 655 THR cc_start: 0.8249 (t) cc_final: 0.8013 (t) REVERT: A 786 LEU cc_start: 0.7201 (mt) cc_final: 0.6800 (mt) REVERT: A 915 TRP cc_start: 0.7484 (t60) cc_final: 0.7214 (t60) REVERT: A 940 ASN cc_start: 0.7911 (t0) cc_final: 0.7273 (p0) REVERT: A 1043 ARG cc_start: 0.6465 (mmt180) cc_final: 0.5971 (tpp80) outliers start: 20 outliers final: 12 residues processed: 152 average time/residue: 0.1900 time to fit residues: 41.0220 Evaluate side-chains 132 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 1046 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN A 477 ASN A 480 ASN A 616 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.141762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.114217 restraints weight = 18646.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.113863 restraints weight = 13922.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.115721 restraints weight = 10774.076| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8790 Z= 0.292 Angle : 0.662 12.809 12109 Z= 0.346 Chirality : 0.043 0.162 1367 Planarity : 0.004 0.034 1338 Dihedral : 19.969 179.856 1811 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 2.85 % Allowed : 17.59 % Favored : 79.56 % 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: -0.31 (0.28), residues: 916 helix: 1.71 (0.23), residues: 499 sheet: -2.29 (0.47), residues: 94 loop : -2.75 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 915 HIS 0.006 0.001 HIS A 952 PHE 0.047 0.003 PHE A 80 TYR 0.014 0.002 TYR A 541 ARG 0.003 0.000 ARG A1043 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6316 (tpt) cc_final: 0.5933 (tpt) REVERT: A 34 MET cc_start: 0.8084 (mmm) cc_final: 0.7671 (mmm) REVERT: A 78 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7128 (t0) REVERT: A 159 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6900 (tp30) REVERT: A 539 GLU cc_start: 0.4470 (tp30) cc_final: 0.3171 (tp30) REVERT: A 780 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: A 929 MET cc_start: 0.7573 (mtp) cc_final: 0.7198 (mtm) REVERT: A 940 ASN cc_start: 0.8011 (t0) cc_final: 0.7303 (p0) REVERT: A 948 ASP cc_start: 0.7436 (t0) cc_final: 0.7154 (t0) REVERT: A 1043 ARG cc_start: 0.6683 (mmt180) cc_final: 0.6221 (tpp80) outliers start: 22 outliers final: 16 residues processed: 143 average time/residue: 0.1852 time to fit residues: 38.0773 Evaluate side-chains 135 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 951 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 28 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.143872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.116908 restraints weight = 18732.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.118481 restraints weight = 15934.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.119635 restraints weight = 11147.207| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8790 Z= 0.217 Angle : 0.643 13.078 12109 Z= 0.328 Chirality : 0.042 0.191 1367 Planarity : 0.003 0.032 1338 Dihedral : 19.920 179.387 1811 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.85 % Allowed : 19.02 % Favored : 78.14 % 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: -0.25 (0.28), residues: 916 helix: 1.76 (0.23), residues: 498 sheet: -2.05 (0.50), residues: 85 loop : -2.79 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 915 HIS 0.003 0.001 HIS A 952 PHE 0.021 0.002 PHE A 743 TYR 0.019 0.001 TYR A 301 ARG 0.002 0.000 ARG A 769 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6389 (tpt) cc_final: 0.6019 (tpt) REVERT: A 34 MET cc_start: 0.8010 (mmm) cc_final: 0.7663 (mmm) REVERT: A 159 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6895 (tp30) REVERT: A 780 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: A 940 ASN cc_start: 0.7794 (t0) cc_final: 0.7221 (p0) REVERT: A 948 ASP cc_start: 0.7178 (t0) cc_final: 0.6919 (t0) REVERT: A 1043 ARG cc_start: 0.6461 (mmt180) cc_final: 0.5981 (tpp80) outliers start: 22 outliers final: 16 residues processed: 135 average time/residue: 0.1847 time to fit residues: 36.1734 Evaluate side-chains 130 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 1046 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 37 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 47 optimal weight: 0.0980 chunk 92 optimal weight: 6.9990 chunk 58 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** A 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.144450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.117543 restraints weight = 18820.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.118792 restraints weight = 15654.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.119909 restraints weight = 12132.318| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8790 Z= 0.211 Angle : 0.629 12.786 12109 Z= 0.322 Chirality : 0.041 0.240 1367 Planarity : 0.003 0.031 1338 Dihedral : 19.894 179.312 1811 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.33 % Allowed : 19.28 % Favored : 78.40 % 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: -0.26 (0.28), residues: 916 helix: 1.74 (0.23), residues: 499 sheet: -1.95 (0.52), residues: 75 loop : -2.82 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 915 HIS 0.003 0.001 HIS A 24 PHE 0.033 0.002 PHE A 743 TYR 0.012 0.001 TYR A 963 ARG 0.005 0.000 ARG A 787 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6401 (tpt) cc_final: 0.6027 (tpt) REVERT: A 78 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7349 (t0) REVERT: A 159 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6879 (tp30) REVERT: A 758 MET cc_start: 0.8108 (mmm) cc_final: 0.7575 (mmt) REVERT: A 780 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: A 940 ASN cc_start: 0.7818 (t0) cc_final: 0.7223 (p0) REVERT: A 948 ASP cc_start: 0.7224 (t0) cc_final: 0.6984 (t0) REVERT: A 1043 ARG cc_start: 0.6423 (mmt180) cc_final: 0.5977 (tpp80) outliers start: 18 outliers final: 15 residues processed: 133 average time/residue: 0.1817 time to fit residues: 35.0866 Evaluate side-chains 135 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 30.0000 chunk 13 optimal weight: 0.0980 chunk 56 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.145970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.118672 restraints weight = 18551.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.120537 restraints weight = 14288.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.121526 restraints weight = 10318.737| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8790 Z= 0.185 Angle : 0.630 12.734 12109 Z= 0.321 Chirality : 0.041 0.206 1367 Planarity : 0.003 0.031 1338 Dihedral : 19.853 178.245 1811 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.20 % Allowed : 19.92 % Favored : 77.88 % 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: -0.24 (0.28), residues: 916 helix: 1.72 (0.23), residues: 501 sheet: -1.98 (0.57), residues: 65 loop : -2.76 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP A 79 HIS 0.002 0.000 HIS A 528 PHE 0.034 0.002 PHE A 743 TYR 0.024 0.001 TYR A1007 ARG 0.002 0.000 ARG A 769 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 19 MET cc_start: 0.6286 (tpt) cc_final: 0.5964 (tpt) REVERT: A 78 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7454 (t0) REVERT: A 159 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6945 (tp30) REVERT: A 537 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6848 (mm) REVERT: A 758 MET cc_start: 0.8167 (mmm) cc_final: 0.7852 (mmt) REVERT: A 918 ARG cc_start: 0.6704 (mmm-85) cc_final: 0.6455 (mmm-85) REVERT: A 940 ASN cc_start: 0.7834 (t0) cc_final: 0.7086 (p0) REVERT: A 996 TYR cc_start: 0.5923 (m-10) cc_final: 0.5577 (m-10) REVERT: A 1043 ARG cc_start: 0.6462 (mmt180) cc_final: 0.6013 (tpp80) outliers start: 17 outliers final: 13 residues processed: 135 average time/residue: 0.1904 time to fit residues: 36.7402 Evaluate side-chains 131 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 28 optimal weight: 6.9990 chunk 78 optimal weight: 0.0570 chunk 74 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 overall best weight: 2.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.141814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.116456 restraints weight = 18800.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.117848 restraints weight = 15030.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.118689 restraints weight = 11332.103| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8790 Z= 0.291 Angle : 0.699 12.725 12109 Z= 0.360 Chirality : 0.044 0.217 1367 Planarity : 0.004 0.038 1338 Dihedral : 19.929 177.397 1811 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.20 % Allowed : 20.70 % Favored : 77.10 % 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: -0.46 (0.28), residues: 916 helix: 1.52 (0.23), residues: 499 sheet: -1.78 (0.59), residues: 72 loop : -2.88 (0.29), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.004 TRP A 79 HIS 0.006 0.001 HIS A 952 PHE 0.033 0.002 PHE A 743 TYR 0.020 0.002 TYR A 995 ARG 0.003 0.000 ARG A 769 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 19 MET cc_start: 0.6380 (tpt) cc_final: 0.5974 (tpt) REVERT: A 34 MET cc_start: 0.8145 (mmm) cc_final: 0.7818 (mmm) REVERT: A 78 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7623 (t0) REVERT: A 159 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7004 (tp30) REVERT: A 753 LEU cc_start: 0.7789 (tt) cc_final: 0.7555 (tt) REVERT: A 940 ASN cc_start: 0.7808 (t0) cc_final: 0.7216 (p0) REVERT: A 996 TYR cc_start: 0.5610 (m-10) cc_final: 0.5326 (m-10) REVERT: A 1038 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.5648 (mp) REVERT: A 1043 ARG cc_start: 0.6446 (mmt180) cc_final: 0.6043 (tpp80) outliers start: 17 outliers final: 15 residues processed: 129 average time/residue: 0.2003 time to fit residues: 37.9221 Evaluate side-chains 131 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1046 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.145116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.119927 restraints weight = 18640.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.121642 restraints weight = 14369.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.122520 restraints weight = 10776.353| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8790 Z= 0.194 Angle : 0.668 12.752 12109 Z= 0.340 Chirality : 0.041 0.191 1367 Planarity : 0.004 0.043 1338 Dihedral : 19.843 176.825 1811 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.81 % Allowed : 21.35 % Favored : 76.84 % 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: -0.40 (0.28), residues: 916 helix: 1.58 (0.23), residues: 499 sheet: -2.04 (0.56), residues: 75 loop : -2.79 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP A 79 HIS 0.002 0.001 HIS A 528 PHE 0.035 0.002 PHE A 743 TYR 0.012 0.001 TYR A 963 ARG 0.008 0.000 ARG A 769 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2371.55 seconds wall clock time: 43 minutes 41.45 seconds (2621.45 seconds total)