Starting phenix.real_space_refine on Sat Dec 28 14:47:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w64_21552/12_2024/6w64_21552.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w64_21552/12_2024/6w64_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_21552/12_2024/6w64_21552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w64_21552/12_2024/6w64_21552.map" model { file = "/net/cci-nas-00/data/ceres_data/6w64_21552/12_2024/6w64_21552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w64_21552/12_2024/6w64_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-5532/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: 5.57, per 1000 atoms: 0.65 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: 2.53 Conformation dependent library (CDL) restraints added in 929.5 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: 3.23 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: 3.66 Time building geometry restraints manager: 2.81 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: 0.450 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.130 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.220 ------------------------------------------------------------------------------- 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 : 0.938 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: 0.2435 time to fit residues: 82.4365 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 : 1.039 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 : 0.984 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: 0.6365 (tpt) cc_final: 0.5962 (tpt) REVERT: A 159 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7042 (tp30) REVERT: A 460 LYS cc_start: 0.8616 (tttm) cc_final: 0.8400 (ttmt) REVERT: A 539 GLU cc_start: 0.4813 (tp30) cc_final: 0.3519 (tp30) REVERT: A 918 ARG cc_start: 0.6983 (mmm-85) cc_final: 0.6733 (mmm-85) REVERT: A 940 ASN cc_start: 0.8038 (t0) cc_final: 0.7398 (p0) REVERT: A 948 ASP cc_start: 0.7437 (t0) cc_final: 0.7217 (t0) outliers start: 24 outliers final: 16 residues processed: 159 average time/residue: 0.2073 time to fit residues: 45.6308 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 : 0.864 ------------------------------------------------------------------------------- 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 48 optimal weight: 0.9990 chunk 27 optimal weight: 40.0000 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3704 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= 0.257 Angle : 0.665 12.367 12109 Z= 0.346 Chirality : 0.042 0.164 1367 Planarity : 0.004 0.056 1338 Dihedral : 19.952 177.893 1811 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % 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: -0.46 (0.28), residues: 916 helix: 1.60 (0.23), residues: 499 sheet: -2.65 (0.48), residues: 94 loop : -2.73 (0.32), residues: 323 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 0.041 0.002 PHE A 80 TYR 0.024 0.002 TYR A 406 ARG 0.017 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 162 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6167 (tpt) cc_final: 0.5808 (tpt) REVERT: A 116 TYR cc_start: 0.8430 (t80) cc_final: 0.8168 (t80) REVERT: A 159 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6865 (tp30) REVERT: A 315 MET cc_start: 0.7669 (mmt) cc_final: 0.7468 (mmt) REVERT: A 539 GLU cc_start: 0.4855 (tp30) cc_final: 0.3645 (tp30) REVERT: A 940 ASN cc_start: 0.8007 (t0) cc_final: 0.7450 (p0) REVERT: A 948 ASP cc_start: 0.7262 (t0) cc_final: 0.6977 (t0) REVERT: A 959 PHE cc_start: 0.7784 (m-80) cc_final: 0.7449 (m-80) outliers start: 22 outliers final: 14 residues processed: 152 average time/residue: 0.2069 time to fit residues: 44.0933 Evaluate side-chains 137 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 86 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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 A 711 HIS A 895 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4113 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= 0.276 Angle : 0.675 13.228 12109 Z= 0.348 Chirality : 0.043 0.164 1367 Planarity : 0.004 0.035 1338 Dihedral : 20.062 179.733 1811 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 3.36 % Allowed : 15.91 % Favored : 80.72 % 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: -0.54 (0.28), residues: 916 helix: 1.50 (0.23), residues: 501 sheet: -2.56 (0.50), residues: 92 loop : -2.78 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 915 HIS 0.006 0.001 HIS A 952 PHE 0.025 0.002 PHE A 743 TYR 0.023 0.002 TYR A 406 ARG 0.003 0.001 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 157 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6323 (tpt) cc_final: 0.5962 (tpt) REVERT: A 116 TYR cc_start: 0.8366 (t80) cc_final: 0.8062 (t80) REVERT: A 315 MET cc_start: 0.7747 (mmt) cc_final: 0.7534 (mmt) REVERT: A 539 GLU cc_start: 0.4796 (tp30) cc_final: 0.3501 (tp30) REVERT: A 940 ASN cc_start: 0.8091 (t0) cc_final: 0.7478 (p0) REVERT: A 948 ASP cc_start: 0.7361 (t0) cc_final: 0.7078 (t0) REVERT: A 1043 ARG cc_start: 0.6074 (mmt180) cc_final: 0.5427 (tpp80) outliers start: 26 outliers final: 18 residues processed: 146 average time/residue: 0.2011 time to fit residues: 41.7612 Evaluate side-chains 138 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 375 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 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 684 VAL 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 52 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 480 ASN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8790 Z= 0.382 Angle : 0.749 13.184 12109 Z= 0.392 Chirality : 0.046 0.252 1367 Planarity : 0.004 0.035 1338 Dihedral : 20.274 176.871 1811 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 4.40 % Allowed : 16.17 % Favored : 79.43 % 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: -0.81 (0.28), residues: 916 helix: 1.24 (0.23), residues: 501 sheet: -2.55 (0.49), residues: 94 loop : -2.86 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 915 HIS 0.008 0.002 HIS A 952 PHE 0.037 0.003 PHE A 80 TYR 0.021 0.002 TYR A 406 ARG 0.004 0.001 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 163 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 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: 0.6286 (tpt) cc_final: 0.5925 (tpt) REVERT: A 315 MET cc_start: 0.7846 (mmt) cc_final: 0.7582 (mmt) REVERT: A 539 GLU cc_start: 0.4484 (tp30) cc_final: 0.2883 (tp30) REVERT: A 780 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: A 940 ASN cc_start: 0.8037 (t0) cc_final: 0.7439 (p0) REVERT: A 948 ASP cc_start: 0.7519 (t0) cc_final: 0.7290 (t0) REVERT: A 1038 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.5737 (mp) REVERT: A 1043 ARG cc_start: 0.6153 (mmt180) cc_final: 0.5498 (tpp80) REVERT: A 1053 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6960 (ptpp) outliers start: 34 outliers final: 23 residues processed: 149 average time/residue: 0.2078 time to fit residues: 43.0512 Evaluate side-chains 141 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET 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 375 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 521 THR 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 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 Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1053 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 ASN A 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4811 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= 0.212 Angle : 0.663 13.210 12109 Z= 0.340 Chirality : 0.042 0.192 1367 Planarity : 0.004 0.030 1338 Dihedral : 20.158 177.394 1811 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.72 % Allowed : 18.50 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.28), residues: 916 helix: 1.45 (0.23), residues: 499 sheet: -2.13 (0.54), residues: 86 loop : -2.86 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 915 HIS 0.003 0.001 HIS A 24 PHE 0.048 0.002 PHE A 80 TYR 0.023 0.002 TYR A 301 ARG 0.002 0.000 ARG A 769 *********************** 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 150 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6286 (tpt) cc_final: 0.5963 (tpt) REVERT: A 539 GLU cc_start: 0.4843 (tp30) cc_final: 0.3499 (tp30) REVERT: A 758 MET cc_start: 0.7625 (tpp) cc_final: 0.7370 (mmt) REVERT: A 780 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7294 (pt0) REVERT: A 940 ASN cc_start: 0.7892 (t0) cc_final: 0.7369 (p0) REVERT: A 948 ASP cc_start: 0.7237 (t0) cc_final: 0.7026 (t0) REVERT: A 1043 ARG cc_start: 0.5953 (mmt180) cc_final: 0.5419 (tpp80) outliers start: 21 outliers final: 16 residues processed: 144 average time/residue: 0.1848 time to fit residues: 37.8294 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 : 0.975 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 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 102 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.5022 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= 0.273 Angle : 0.672 13.105 12109 Z= 0.349 Chirality : 0.043 0.173 1367 Planarity : 0.004 0.031 1338 Dihedral : 20.215 176.675 1811 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.36 % Allowed : 18.89 % Favored : 77.75 % 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: -0.69 (0.28), residues: 916 helix: 1.36 (0.23), residues: 501 sheet: -2.08 (0.54), residues: 74 loop : -2.99 (0.30), residues: 341 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 0.041 0.002 PHE A 80 TYR 0.014 0.002 TYR A 646 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 150 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6338 (tpt) cc_final: 0.5998 (tpt) REVERT: A 539 GLU cc_start: 0.4465 (tp30) cc_final: 0.3067 (tp30) REVERT: A 780 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: A 915 TRP cc_start: 0.7618 (t60) cc_final: 0.7343 (t60) REVERT: A 940 ASN cc_start: 0.7895 (t0) cc_final: 0.7317 (p0) REVERT: A 1038 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.5742 (mp) REVERT: A 1043 ARG cc_start: 0.6000 (mmt180) cc_final: 0.5479 (tpp80) outliers start: 26 outliers final: 19 residues processed: 141 average time/residue: 0.1945 time to fit residues: 39.2014 Evaluate side-chains 136 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.5219 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= 0.226 Angle : 0.657 12.965 12109 Z= 0.335 Chirality : 0.042 0.172 1367 Planarity : 0.004 0.029 1338 Dihedral : 20.222 177.224 1811 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.72 % Allowed : 20.05 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.28), residues: 916 helix: 1.51 (0.23), residues: 499 sheet: -1.93 (0.57), residues: 76 loop : -2.92 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 915 HIS 0.003 0.001 HIS A 24 PHE 0.028 0.002 PHE A 743 TYR 0.014 0.002 TYR A 301 ARG 0.002 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: 21 poor density : 129 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6356 (tpt) cc_final: 0.6012 (tpt) REVERT: A 476 PHE cc_start: 0.7293 (m-80) cc_final: 0.7084 (m-80) REVERT: A 539 GLU cc_start: 0.4687 (tp30) cc_final: 0.3380 (tp30) REVERT: A 780 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: A 940 ASN cc_start: 0.7878 (t0) cc_final: 0.7299 (p0) REVERT: A 1043 ARG cc_start: 0.6139 (mmt180) cc_final: 0.5628 (tpp80) outliers start: 21 outliers final: 17 residues processed: 141 average time/residue: 0.1914 time to fit residues: 38.2674 Evaluate side-chains 132 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8790 Z= 0.386 Angle : 0.762 13.228 12109 Z= 0.395 Chirality : 0.046 0.186 1367 Planarity : 0.004 0.036 1338 Dihedral : 20.369 176.373 1811 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 3.36 % Allowed : 19.53 % 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: -0.89 (0.28), residues: 916 helix: 1.20 (0.23), residues: 501 sheet: -2.20 (0.55), residues: 80 loop : -3.08 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 915 HIS 0.009 0.001 HIS A 952 PHE 0.028 0.003 PHE A 743 TYR 0.015 0.002 TYR A 116 ARG 0.004 0.001 ARG A 535 *********************** 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 146 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6389 (tpt) cc_final: 0.6044 (tpt) REVERT: A 78 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7409 (t0) REVERT: A 539 GLU cc_start: 0.4784 (tp30) cc_final: 0.3580 (mm-30) REVERT: A 780 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7703 (pm20) REVERT: A 929 MET cc_start: 0.7629 (mtt) cc_final: 0.7230 (mtp) REVERT: A 940 ASN cc_start: 0.7921 (t0) cc_final: 0.7289 (p0) REVERT: A 948 ASP cc_start: 0.7607 (t0) cc_final: 0.6871 (m-30) REVERT: A 1038 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.5760 (mp) REVERT: A 1043 ARG cc_start: 0.6216 (mmt180) cc_final: 0.5670 (tpp80) outliers start: 26 outliers final: 20 residues processed: 138 average time/residue: 0.2032 time to fit residues: 39.6161 Evaluate side-chains 138 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR 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 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 593 MET 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 780 GLU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 800 SER 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 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 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.5596 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= 0.197 Angle : 0.684 12.759 12109 Z= 0.348 Chirality : 0.041 0.193 1367 Planarity : 0.004 0.043 1338 Dihedral : 20.117 178.550 1811 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.46 % Allowed : 20.70 % 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: -0.65 (0.28), residues: 916 helix: 1.44 (0.23), residues: 499 sheet: -2.12 (0.59), residues: 62 loop : -3.02 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 915 HIS 0.002 0.001 HIS A 384 PHE 0.032 0.002 PHE A 743 TYR 0.014 0.001 TYR A 640 ARG 0.003 0.000 ARG A 22 ********************** 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 148 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6245 (tpt) cc_final: 0.5926 (tpt) REVERT: A 491 PRO cc_start: 0.6494 (Cg_exo) cc_final: 0.6183 (Cg_endo) REVERT: A 539 GLU cc_start: 0.4834 (tp30) cc_final: 0.3547 (tp30) REVERT: A 929 MET cc_start: 0.7409 (mtt) cc_final: 0.7016 (mtp) REVERT: A 940 ASN cc_start: 0.7853 (t0) cc_final: 0.7276 (p0) REVERT: A 1038 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.5691 (mp) outliers start: 19 outliers final: 12 residues processed: 138 average time/residue: 0.1972 time to fit residues: 39.3158 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 : 0.967 ------------------------------------------------------------------------------- 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 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 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 854 LEU 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 23 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 477 ASN A 616 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.142040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.116879 restraints weight = 18403.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.118807 restraints weight = 14407.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.119520 restraints weight = 10256.459| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8790 Z= 0.217 Angle : 0.696 12.363 12109 Z= 0.352 Chirality : 0.043 0.257 1367 Planarity : 0.004 0.039 1338 Dihedral : 19.976 179.277 1811 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.33 % Allowed : 21.09 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.28), residues: 916 helix: 1.38 (0.23), residues: 500 sheet: -2.05 (0.54), residues: 72 loop : -2.99 (0.30), residues: 344 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 0.034 0.002 PHE A 743 TYR 0.026 0.002 TYR A1007 ARG 0.007 0.000 ARG A 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1774.65 seconds wall clock time: 33 minutes 56.88 seconds (2036.88 seconds total)