Starting phenix.real_space_refine on Thu Mar 13 06:11:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w64_21552/03_2025/6w64_21552.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w64_21552/03_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_21552/03_2025/6w64_21552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w64_21552/03_2025/6w64_21552.map" model { file = "/net/cci-nas-00/data/ceres_data/6w64_21552/03_2025/6w64_21552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w64_21552/03_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-5624/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: 5.69, 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: 2.40 Conformation dependent library (CDL) restraints added in 888.0 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: 3.14 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: 3.51 Time building geometry restraints manager: 2.78 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: 0.310 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 26.120 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.940 ------------------------------------------------------------------------------- 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 : 0.911 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: 0.2508 time to fit residues: 84.8440 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 : 0.730 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.114125 restraints weight = 18670.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.116034 restraints weight = 16559.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.116719 restraints weight = 10741.610| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 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 : 0.834 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: 0.6326 (tpt) cc_final: 0.5918 (tpt) REVERT: A 159 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7042 (tp30) REVERT: A 460 LYS cc_start: 0.8603 (tttm) cc_final: 0.8402 (ttmt) REVERT: A 539 GLU cc_start: 0.4817 (tp30) cc_final: 0.3522 (tp30) REVERT: A 918 ARG cc_start: 0.6996 (mmm-85) cc_final: 0.6742 (mmm-85) REVERT: A 940 ASN cc_start: 0.8046 (t0) cc_final: 0.7388 (p0) REVERT: A 948 ASP cc_start: 0.7458 (t0) cc_final: 0.7240 (t0) outliers start: 24 outliers final: 16 residues processed: 159 average time/residue: 0.2016 time to fit residues: 44.3411 Evaluate side-chains 131 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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: 6.9990 chunk 72 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 85 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.142259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.114672 restraints weight = 18799.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.115418 restraints weight = 14001.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.116794 restraints weight = 10442.796| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3715 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= 0.278 Angle : 0.674 12.405 12109 Z= 0.352 Chirality : 0.043 0.164 1367 Planarity : 0.004 0.057 1338 Dihedral : 19.965 178.104 1811 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.85 % Allowed : 14.88 % Favored : 82.28 % 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: -0.51 (0.28), residues: 916 helix: 1.56 (0.23), residues: 498 sheet: -2.68 (0.48), residues: 94 loop : -2.73 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 915 HIS 0.005 0.001 HIS A 952 PHE 0.038 0.002 PHE A 80 TYR 0.024 0.002 TYR A 406 ARG 0.010 0.001 ARG A 26 *********************** 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 161 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6061 (tpt) cc_final: 0.5699 (tpt) REVERT: A 116 TYR cc_start: 0.8516 (t80) cc_final: 0.8270 (t80) REVERT: A 159 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6886 (tp30) REVERT: A 460 LYS cc_start: 0.8564 (tttm) cc_final: 0.8322 (ttmt) REVERT: A 539 GLU cc_start: 0.4865 (tp30) cc_final: 0.3633 (tp30) REVERT: A 940 ASN cc_start: 0.8049 (t0) cc_final: 0.7448 (p0) REVERT: A 948 ASP cc_start: 0.7431 (t0) cc_final: 0.7122 (t0) REVERT: A 959 PHE cc_start: 0.8037 (m-80) cc_final: 0.7681 (m-80) outliers start: 22 outliers final: 14 residues processed: 152 average time/residue: 0.1994 time to fit residues: 42.3963 Evaluate side-chains 138 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 448 ILE 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 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: 1.9990 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: 2.9990 chunk 28 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.143462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.116353 restraints weight = 18599.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.116138 restraints weight = 14339.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.117314 restraints weight = 12318.020| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8790 Z= 0.219 Angle : 0.640 13.103 12109 Z= 0.329 Chirality : 0.041 0.164 1367 Planarity : 0.004 0.032 1338 Dihedral : 19.994 179.321 1811 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.10 % Allowed : 15.91 % Favored : 80.98 % 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: -0.43 (0.28), residues: 916 helix: 1.63 (0.23), residues: 499 sheet: -2.64 (0.49), residues: 95 loop : -2.73 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 915 HIS 0.004 0.001 HIS A 24 PHE 0.024 0.002 PHE A 80 TYR 0.023 0.002 TYR A 406 ARG 0.004 0.001 ARG A 22 *********************** 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 164 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6276 (tpt) cc_final: 0.5952 (tpt) REVERT: A 37 LEU cc_start: 0.8269 (mt) cc_final: 0.7947 (mt) REVERT: A 116 TYR cc_start: 0.8394 (t80) cc_final: 0.8082 (t80) REVERT: A 460 LYS cc_start: 0.8559 (tttm) cc_final: 0.8331 (ttmt) REVERT: A 476 PHE cc_start: 0.7267 (m-80) cc_final: 0.7007 (m-80) REVERT: A 537 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6816 (mm) REVERT: A 539 GLU cc_start: 0.4773 (tp30) cc_final: 0.3563 (tp30) REVERT: A 940 ASN cc_start: 0.8007 (t0) cc_final: 0.7392 (p0) REVERT: A 948 ASP cc_start: 0.7278 (t0) cc_final: 0.6996 (t0) outliers start: 24 outliers final: 14 residues processed: 153 average time/residue: 0.1938 time to fit residues: 42.0607 Evaluate side-chains 138 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 ASN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.139452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.113506 restraints weight = 18810.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.114764 restraints weight = 13432.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.115752 restraints weight = 10553.446| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.4521 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= 0.320 Angle : 0.706 13.052 12109 Z= 0.367 Chirality : 0.044 0.196 1367 Planarity : 0.004 0.036 1338 Dihedral : 20.151 178.598 1811 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 3.36 % Allowed : 17.08 % 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: -0.61 (0.28), residues: 916 helix: 1.46 (0.23), residues: 499 sheet: -2.56 (0.48), residues: 94 loop : -2.81 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 915 HIS 0.007 0.001 HIS A 952 PHE 0.028 0.002 PHE A 743 TYR 0.021 0.002 TYR A 406 ARG 0.003 0.000 ARG A 535 *********************** 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 152 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6340 (tpt) cc_final: 0.5999 (tpt) REVERT: A 37 LEU cc_start: 0.8506 (mt) cc_final: 0.8247 (mt) REVERT: A 460 LYS cc_start: 0.8560 (tttm) cc_final: 0.8359 (ttmt) REVERT: A 520 LYS cc_start: 0.9147 (mmtt) cc_final: 0.8918 (mmtt) REVERT: A 539 GLU cc_start: 0.4386 (tp30) cc_final: 0.2938 (tp30) REVERT: A 753 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7970 (tt) REVERT: A 780 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7412 (pt0) REVERT: A 940 ASN cc_start: 0.8082 (t0) cc_final: 0.7451 (p0) REVERT: A 948 ASP cc_start: 0.7540 (t0) cc_final: 0.7318 (t0) REVERT: A 1043 ARG cc_start: 0.6114 (mmt180) cc_final: 0.5462 (tpp80) outliers start: 26 outliers final: 18 residues processed: 142 average time/residue: 0.1940 time to fit residues: 38.9317 Evaluate side-chains 134 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET 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 375 THR Chi-restraints excluded: chain A residue 440 LYS 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 684 VAL Chi-restraints excluded: chain A residue 753 LEU 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 880 LEU Chi-restraints excluded: chain A residue 951 VAL 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: 2.9990 chunk 56 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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 477 ASN A 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.140432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.114417 restraints weight = 18539.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.113886 restraints weight = 16603.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.115855 restraints weight = 12779.155| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8790 Z= 0.277 Angle : 0.673 13.124 12109 Z= 0.349 Chirality : 0.043 0.180 1367 Planarity : 0.004 0.034 1338 Dihedral : 20.117 178.068 1811 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 3.49 % Allowed : 17.46 % Favored : 79.04 % 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: -0.60 (0.28), residues: 916 helix: 1.44 (0.23), residues: 498 sheet: -2.21 (0.52), residues: 84 loop : -2.89 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 915 HIS 0.005 0.001 HIS A 952 PHE 0.028 0.002 PHE A 743 TYR 0.017 0.002 TYR A 646 ARG 0.002 0.000 ARG A 535 *********************** 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 155 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6393 (tpt) cc_final: 0.6029 (tpt) REVERT: A 520 LYS cc_start: 0.9099 (mmtt) cc_final: 0.8819 (mmtt) REVERT: A 539 GLU cc_start: 0.4430 (tp30) cc_final: 0.2976 (tp30) REVERT: A 753 LEU cc_start: 0.8119 (tt) cc_final: 0.7863 (tt) REVERT: A 780 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7287 (pt0) REVERT: A 940 ASN cc_start: 0.7879 (t0) cc_final: 0.7309 (p0) REVERT: A 1038 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.5614 (mp) REVERT: A 1043 ARG cc_start: 0.6092 (mmt180) cc_final: 0.5486 (tpp80) outliers start: 27 outliers final: 19 residues processed: 147 average time/residue: 0.1884 time to fit residues: 39.5544 Evaluate side-chains 137 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 375 THR Chi-restraints excluded: chain A residue 440 LYS 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 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 684 VAL 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 Chi-restraints excluded: chain A residue 1038 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 28 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 48 optimal weight: 0.4980 chunk 76 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 480 ASN ** A 616 ASN ** 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 = 0.4079 r_free = 0.4079 target = 0.139921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.114977 restraints weight = 18562.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.116627 restraints weight = 14523.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.117513 restraints weight = 11053.515| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8790 Z= 0.279 Angle : 0.683 13.048 12109 Z= 0.355 Chirality : 0.044 0.229 1367 Planarity : 0.004 0.032 1338 Dihedral : 20.161 177.283 1811 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 3.36 % Allowed : 18.37 % Favored : 78.27 % 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: 1.39 (0.23), residues: 498 sheet: -2.12 (0.55), residues: 72 loop : -2.96 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 915 HIS 0.005 0.001 HIS A 952 PHE 0.028 0.002 PHE A 743 TYR 0.014 0.002 TYR A 646 ARG 0.002 0.000 ARG A 652 *********************** 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: 26 poor density : 120 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6318 (tpt) cc_final: 0.5971 (tpt) REVERT: A 520 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8704 (mmtt) REVERT: A 539 GLU cc_start: 0.4532 (tp30) cc_final: 0.3108 (tp30) REVERT: A 753 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7772 (tt) REVERT: A 780 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7526 (pm20) REVERT: A 929 MET cc_start: 0.7363 (mtp) cc_final: 0.7094 (mtm) REVERT: A 940 ASN cc_start: 0.7932 (t0) cc_final: 0.7390 (p0) REVERT: A 948 ASP cc_start: 0.7145 (t0) cc_final: 0.6517 (m-30) REVERT: A 1038 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.5691 (mp) REVERT: A 1043 ARG cc_start: 0.5972 (mmt180) cc_final: 0.5440 (tpp80) outliers start: 26 outliers final: 17 residues processed: 136 average time/residue: 0.1809 time to fit residues: 35.3861 Evaluate side-chains 135 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 375 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 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 684 VAL Chi-restraints excluded: chain A residue 753 LEU 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 951 VAL Chi-restraints excluded: chain A residue 1038 LEU 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: 0.8980 chunk 81 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 372 ASN A 480 ASN A 616 ASN ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.143049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.118350 restraints weight = 18653.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.120030 restraints weight = 14373.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.120788 restraints weight = 10737.899| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.5162 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= 0.204 Angle : 0.638 12.917 12109 Z= 0.325 Chirality : 0.041 0.180 1367 Planarity : 0.004 0.030 1338 Dihedral : 20.083 177.816 1811 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % 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: -0.44 (0.28), residues: 916 helix: 1.58 (0.23), residues: 500 sheet: -1.98 (0.56), residues: 76 loop : -2.90 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 915 HIS 0.003 0.001 HIS A 952 PHE 0.030 0.002 PHE A 743 TYR 0.012 0.001 TYR A 646 ARG 0.003 0.000 ARG A 769 *********************** 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 150 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6292 (tpt) cc_final: 0.5935 (tpt) REVERT: A 520 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8760 (mmtt) REVERT: A 539 GLU cc_start: 0.4750 (tp30) cc_final: 0.3482 (tp30) REVERT: A 940 ASN cc_start: 0.7875 (t0) cc_final: 0.7280 (p0) REVERT: A 1038 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5522 (mp) outliers start: 22 outliers final: 16 residues processed: 140 average time/residue: 0.1869 time to fit residues: 37.1517 Evaluate side-chains 134 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 375 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 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 854 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1038 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 13 optimal weight: 0.0570 chunk 56 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.3500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN ** 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 = 0.4129 r_free = 0.4129 target = 0.143181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.116015 restraints weight = 18553.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.117257 restraints weight = 15546.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.118377 restraints weight = 11801.902| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.5333 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= 0.213 Angle : 0.650 12.990 12109 Z= 0.333 Chirality : 0.042 0.196 1367 Planarity : 0.004 0.029 1338 Dihedral : 20.134 178.916 1811 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.59 % Allowed : 19.79 % Favored : 77.62 % 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: -0.48 (0.28), residues: 916 helix: 1.53 (0.23), residues: 500 sheet: -1.86 (0.55), residues: 76 loop : -2.93 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 915 HIS 0.003 0.001 HIS A 24 PHE 0.030 0.002 PHE A 743 TYR 0.038 0.002 TYR A1007 ARG 0.002 0.000 ARG A 918 *********************** 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 139 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.899 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: 0.6351 (tpt) cc_final: 0.5980 (tpt) REVERT: A 520 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8782 (mmtt) REVERT: A 539 GLU cc_start: 0.4805 (tp30) cc_final: 0.3442 (tp30) REVERT: A 604 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8057 (mp) REVERT: A 940 ASN cc_start: 0.7843 (t0) cc_final: 0.7266 (p0) REVERT: A 996 TYR cc_start: 0.5743 (m-10) cc_final: 0.5408 (m-10) REVERT: A 1038 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.5594 (mp) REVERT: A 1043 ARG cc_start: 0.6634 (mmt180) cc_final: 0.6023 (tpp80) outliers start: 20 outliers final: 15 residues processed: 129 average time/residue: 0.1875 time to fit residues: 34.6746 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 : 0.921 ------------------------------------------------------------------------------- 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 375 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 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 604 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 Chi-restraints excluded: chain A residue 1038 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 28 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 43 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.142553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.115863 restraints weight = 18575.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.117165 restraints weight = 15942.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.118076 restraints weight = 12435.989| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8790 Z= 0.223 Angle : 0.655 12.815 12109 Z= 0.333 Chirality : 0.042 0.195 1367 Planarity : 0.004 0.030 1338 Dihedral : 20.122 179.687 1811 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.46 % Allowed : 19.66 % 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: -0.49 (0.28), residues: 916 helix: 1.53 (0.23), residues: 501 sheet: -1.93 (0.55), residues: 76 loop : -2.96 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 915 HIS 0.003 0.001 HIS A 952 PHE 0.034 0.002 PHE A 743 TYR 0.013 0.001 TYR A 995 ARG 0.002 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 143 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6365 (tpt) cc_final: 0.5974 (tpt) REVERT: A 26 ARG cc_start: 0.6993 (mmp80) cc_final: 0.6645 (mmm160) REVERT: A 520 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8756 (mmtt) REVERT: A 539 GLU cc_start: 0.4661 (tp30) cc_final: 0.3235 (tp30) REVERT: A 940 ASN cc_start: 0.7864 (t0) cc_final: 0.7266 (p0) REVERT: A 996 TYR cc_start: 0.5754 (m-10) cc_final: 0.5487 (m-10) REVERT: A 1038 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.5595 (mp) REVERT: A 1043 ARG cc_start: 0.6532 (mmt180) cc_final: 0.5948 (tpp80) outliers start: 19 outliers final: 16 residues processed: 134 average time/residue: 0.1931 time to fit residues: 36.7166 Evaluate side-chains 137 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET 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 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 854 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1038 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.142414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.115175 restraints weight = 18735.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.116275 restraints weight = 16089.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.117325 restraints weight = 11960.086| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8790 Z= 0.234 Angle : 0.685 12.431 12109 Z= 0.347 Chirality : 0.043 0.188 1367 Planarity : 0.004 0.030 1338 Dihedral : 20.090 179.783 1811 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 2.98 % Allowed : 19.92 % 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: -0.50 (0.28), residues: 916 helix: 1.52 (0.23), residues: 501 sheet: -1.89 (0.54), residues: 76 loop : -2.94 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 915 HIS 0.004 0.001 HIS A 931 PHE 0.036 0.002 PHE A 743 TYR 0.025 0.002 TYR A1007 ARG 0.003 0.000 ARG A 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2505.64 seconds wall clock time: 45 minutes 22.29 seconds (2722.29 seconds total)