Starting phenix.real_space_refine on Mon Apr 8 12:47:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5p_25706/04_2024/7t5p_25706.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5p_25706/04_2024/7t5p_25706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5p_25706/04_2024/7t5p_25706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5p_25706/04_2024/7t5p_25706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5p_25706/04_2024/7t5p_25706.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5p_25706/04_2024/7t5p_25706.pdb" } resolution = 3.4 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= 0.004 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 37 5.16 5 C 4325 2.51 5 N 1157 2.21 5 O 1212 1.98 5 H 6866 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 493": "OD1" <-> "OD2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A GLU 690": "OE1" <-> "OE2" Residue "A PHE 825": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 747": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 873": "OE1" <-> "OE2" Residue "B GLU 887": "OE1" <-> "OE2" Residue "B ASP 974": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13597 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6750 Classifications: {'peptide': 403} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 381} Chain breaks: 2 Chain: "B" Number of atoms: 6847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 6847 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 18, 'TRANS': 400} Chain breaks: 2 Time building chain proxies: 6.31, per 1000 atoms: 0.46 Number of scatterers: 13597 At special positions: 0 Unit cell: (92.988, 74.844, 105.462, 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 37 16.00 O 1212 8.00 N 1157 7.00 C 4325 6.00 H 6866 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1594 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 0 sheets defined 73.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.542A pdb=" N ARG A 433 " --> pdb=" O CYS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.759A pdb=" N LEU A 450 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 461 Processing helix chain 'A' and resid 468 through 481 removed outlier: 3.527A pdb=" N GLU A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 495 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 520 through 538 removed outlier: 3.684A pdb=" N LEU A 524 " --> pdb=" O THR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.653A pdb=" N VAL A 545 " --> pdb=" O ALA A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 Processing helix chain 'A' and resid 565 through 588 Processing helix chain 'A' and resid 595 through 602 removed outlier: 3.836A pdb=" N SER A 602 " --> pdb=" O ASN A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 655 through 678 removed outlier: 3.547A pdb=" N THR A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 676 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASP A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 698 removed outlier: 3.827A pdb=" N SER A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE A 695 " --> pdb=" O MET A 691 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 711 removed outlier: 3.851A pdb=" N ARG A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 729 Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 761 through 787 removed outlier: 4.102A pdb=" N THR A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 802 removed outlier: 3.997A pdb=" N ASP A 797 " --> pdb=" O ILE A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 834 Processing helix chain 'A' and resid 838 through 855 removed outlier: 3.501A pdb=" N ALA A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 779 Processing helix chain 'B' and resid 781 through 790 removed outlier: 3.749A pdb=" N ILE B 785 " --> pdb=" O LYS B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 797 Processing helix chain 'B' and resid 803 through 817 Processing helix chain 'B' and resid 819 through 841 Processing helix chain 'B' and resid 851 through 863 Processing helix chain 'B' and resid 865 through 870 Processing helix chain 'B' and resid 880 through 892 Processing helix chain 'B' and resid 910 through 928 Processing helix chain 'B' and resid 929 through 932 removed outlier: 4.005A pdb=" N TYR B 932 " --> pdb=" O PRO B 929 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 929 through 932' Processing helix chain 'B' and resid 933 through 949 removed outlier: 3.674A pdb=" N LEU B 949 " --> pdb=" O PHE B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 972 Processing helix chain 'B' and resid 974 through 989 Proline residue: B 980 - end of helix Processing helix chain 'B' and resid 992 through 1003 removed outlier: 3.534A pdb=" N LEU B 996 " --> pdb=" O HIS B 992 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B1003 " --> pdb=" O LEU B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1026 Processing helix chain 'B' and resid 1039 through 1051 Processing helix chain 'B' and resid 1052 through 1068 Processing helix chain 'B' and resid 1074 through 1101 removed outlier: 3.632A pdb=" N CYS B1101 " --> pdb=" O GLY B1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 1108 through 1124 removed outlier: 3.729A pdb=" N HIS B1112 " --> pdb=" O GLY B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1157 removed outlier: 3.878A pdb=" N THR B1138 " --> pdb=" O LEU B1134 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 11.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6851 1.03 - 1.23: 18 1.23 - 1.42: 2793 1.42 - 1.61: 4019 1.61 - 1.81: 59 Bond restraints: 13740 Sorted by residual: bond pdb=" CB PRO A 466 " pdb=" CG PRO A 466 " ideal model delta sigma weight residual 1.492 1.561 -0.069 5.00e-02 4.00e+02 1.92e+00 bond pdb=" CB PRO B 871 " pdb=" CG PRO B 871 " ideal model delta sigma weight residual 1.492 1.549 -0.057 5.00e-02 4.00e+02 1.31e+00 bond pdb=" C ILE A 467 " pdb=" N PRO A 468 " ideal model delta sigma weight residual 1.332 1.346 -0.014 1.33e-02 5.65e+03 1.13e+00 bond pdb=" CB PHE A 581 " pdb=" CG PHE A 581 " ideal model delta sigma weight residual 1.502 1.523 -0.021 2.30e-02 1.89e+03 8.57e-01 bond pdb=" CB CYS B 924 " pdb=" SG CYS B 924 " ideal model delta sigma weight residual 1.808 1.778 0.030 3.30e-02 9.18e+02 8.17e-01 ... (remaining 13735 not shown) Histogram of bond angle deviations from ideal: 100.70 - 107.39: 709 107.39 - 114.07: 16315 114.07 - 120.75: 4802 120.75 - 127.44: 3020 127.44 - 134.12: 88 Bond angle restraints: 24934 Sorted by residual: angle pdb=" C GLU A 690 " pdb=" N MET A 691 " pdb=" CA MET A 691 " ideal model delta sigma weight residual 120.31 116.43 3.88 1.52e+00 4.33e-01 6.53e+00 angle pdb=" CA PRO A 466 " pdb=" C PRO A 466 " pdb=" N ILE A 467 " ideal model delta sigma weight residual 114.74 117.23 -2.49 1.03e+00 9.43e-01 5.82e+00 angle pdb=" CA LEU B 949 " pdb=" CB LEU B 949 " pdb=" CG LEU B 949 " ideal model delta sigma weight residual 116.30 124.53 -8.23 3.50e+00 8.16e-02 5.53e+00 angle pdb=" N MET A 691 " pdb=" CA MET A 691 " pdb=" CB MET A 691 " ideal model delta sigma weight residual 110.28 113.71 -3.43 1.55e+00 4.16e-01 4.90e+00 angle pdb=" CA MET A 691 " pdb=" CB MET A 691 " pdb=" CG MET A 691 " ideal model delta sigma weight residual 114.10 118.31 -4.21 2.00e+00 2.50e-01 4.44e+00 ... (remaining 24929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 5505 17.68 - 35.37: 676 35.37 - 53.05: 176 53.05 - 70.74: 38 70.74 - 88.42: 14 Dihedral angle restraints: 6409 sinusoidal: 3555 harmonic: 2854 Sorted by residual: dihedral pdb=" CA ASP B 763 " pdb=" CB ASP B 763 " pdb=" CG ASP B 763 " pdb=" OD1 ASP B 763 " ideal model delta sinusoidal sigma weight residual -30.00 -88.41 58.41 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CG ARG A 718 " pdb=" CD ARG A 718 " pdb=" NE ARG A 718 " pdb=" CZ ARG A 718 " ideal model delta sinusoidal sigma weight residual 180.00 136.68 43.32 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CB GLU B 742 " pdb=" CG GLU B 742 " pdb=" CD GLU B 742 " pdb=" OE1 GLU B 742 " ideal model delta sinusoidal sigma weight residual 0.00 -85.97 85.97 1 3.00e+01 1.11e-03 9.92e+00 ... (remaining 6406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 795 0.035 - 0.070: 206 0.070 - 0.105: 51 0.105 - 0.140: 18 0.140 - 0.175: 1 Chirality restraints: 1071 Sorted by residual: chirality pdb=" CB THR A 476 " pdb=" CA THR A 476 " pdb=" OG1 THR A 476 " pdb=" CG2 THR A 476 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CB VAL A 696 " pdb=" CA VAL A 696 " pdb=" CG1 VAL A 696 " pdb=" CG2 VAL A 696 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE A 699 " pdb=" N ILE A 699 " pdb=" C ILE A 699 " pdb=" CB ILE A 699 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1068 not shown) Planarity restraints: 1952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 467 " -0.037 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO A 468 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 501 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A 502 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 992 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 993 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 993 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 993 " 0.024 5.00e-02 4.00e+02 ... (remaining 1949 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1246 2.20 - 2.80: 28766 2.80 - 3.40: 39043 3.40 - 4.00: 46977 4.00 - 4.60: 73505 Nonbonded interactions: 189537 Sorted by model distance: nonbonded pdb=" O LEU A 736 " pdb="HE21 GLN A 742 " model vdw 1.602 1.850 nonbonded pdb=" O ILE A 725 " pdb=" HG SER A 729 " model vdw 1.612 1.850 nonbonded pdb=" O GLN B 876 " pdb="HH22 ARG B 935 " model vdw 1.621 1.850 nonbonded pdb=" OE1 GLU B 873 " pdb=" H GLU B 873 " model vdw 1.624 1.850 nonbonded pdb=" O LYS B 970 " pdb=" HZ2 LYS B 970 " model vdw 1.666 1.850 ... (remaining 189532 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.190 Extract box with map and model: 2.240 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 45.820 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 0.069 6874 Z= 0.198 Angle : 0.590 8.231 9307 Z= 0.311 Chirality : 0.036 0.175 1071 Planarity : 0.004 0.057 1175 Dihedral : 17.853 88.424 2606 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.39 % Allowed : 32.69 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.29), residues: 810 helix: 1.54 (0.21), residues: 551 sheet: None (None), residues: 0 loop : -1.05 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1006 HIS 0.004 0.001 HIS A 782 PHE 0.026 0.001 PHE A 825 TYR 0.010 0.001 TYR A 554 ARG 0.008 0.000 ARG B1011 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 245 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6788 (mm-30) outliers start: 3 outliers final: 3 residues processed: 246 average time/residue: 0.4398 time to fit residues: 141.0734 Evaluate side-chains 241 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 238 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN B 790 GLN ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 GLN B1005 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6874 Z= 0.224 Angle : 0.573 5.913 9307 Z= 0.309 Chirality : 0.036 0.157 1071 Planarity : 0.004 0.058 1175 Dihedral : 4.537 43.586 885 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.33 % Allowed : 32.04 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.29), residues: 810 helix: 1.57 (0.21), residues: 562 sheet: None (None), residues: 0 loop : -1.03 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 549 HIS 0.004 0.001 HIS A 782 PHE 0.017 0.001 PHE B 840 TYR 0.006 0.001 TYR B1090 ARG 0.006 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 246 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 252 average time/residue: 0.4612 time to fit residues: 150.9916 Evaluate side-chains 252 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 237 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 854 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1008 SER Chi-restraints excluded: chain B residue 1078 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6874 Z= 0.257 Angle : 0.582 6.084 9307 Z= 0.318 Chirality : 0.036 0.157 1071 Planarity : 0.005 0.065 1175 Dihedral : 4.310 23.422 882 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.88 % Allowed : 31.14 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.88 (0.29), residues: 810 helix: 1.28 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.07 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 549 HIS 0.004 0.001 HIS A 782 PHE 0.016 0.001 PHE B 840 TYR 0.007 0.001 TYR A 554 ARG 0.003 0.000 ARG A 679 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 238 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6930 (mm-30) REVERT: B 1125 LYS cc_start: 0.7471 (tmmt) cc_final: 0.7208 (tmmt) outliers start: 30 outliers final: 27 residues processed: 251 average time/residue: 0.4576 time to fit residues: 148.5512 Evaluate side-chains 261 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 234 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 854 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 1008 SER Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1080 GLU Chi-restraints excluded: chain B residue 1095 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.0050 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 0.2980 chunk 78 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 ASN B1068 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6874 Z= 0.193 Angle : 0.549 5.541 9307 Z= 0.291 Chirality : 0.035 0.157 1071 Planarity : 0.004 0.063 1175 Dihedral : 4.189 24.262 882 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.84 % Allowed : 31.78 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.29), residues: 810 helix: 1.58 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -0.91 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1006 HIS 0.004 0.001 HIS A 782 PHE 0.013 0.001 PHE B 840 TYR 0.007 0.001 TYR A 554 ARG 0.005 0.000 ARG B1011 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 240 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6968 (mm-30) REVERT: B 967 ASN cc_start: 0.8410 (m110) cc_final: 0.8070 (m110) REVERT: B 971 ASN cc_start: 0.7621 (m110) cc_final: 0.7311 (m110) REVERT: B 1125 LYS cc_start: 0.7404 (tmmt) cc_final: 0.7166 (tmmt) outliers start: 22 outliers final: 17 residues processed: 251 average time/residue: 0.4517 time to fit residues: 147.2586 Evaluate side-chains 255 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 238 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1008 SER Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1095 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6874 Z= 0.268 Angle : 0.587 5.801 9307 Z= 0.322 Chirality : 0.036 0.155 1071 Planarity : 0.005 0.066 1175 Dihedral : 4.330 23.482 882 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.88 % Allowed : 31.52 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.90 (0.29), residues: 810 helix: 1.29 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -1.06 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 549 HIS 0.004 0.001 HIS A 782 PHE 0.014 0.001 PHE B 840 TYR 0.014 0.001 TYR A 780 ARG 0.005 0.000 ARG B1011 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 235 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7056 (mm-30) REVERT: B 1125 LYS cc_start: 0.7512 (tmmt) cc_final: 0.7264 (tmmt) outliers start: 30 outliers final: 28 residues processed: 245 average time/residue: 0.4731 time to fit residues: 150.9119 Evaluate side-chains 263 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 235 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 854 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 960 ASP Chi-restraints excluded: chain B residue 1008 SER Chi-restraints excluded: chain B residue 1055 ASP Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1095 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6874 Z= 0.222 Angle : 0.567 5.801 9307 Z= 0.305 Chirality : 0.036 0.156 1071 Planarity : 0.004 0.066 1175 Dihedral : 4.278 24.086 882 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.36 % Allowed : 31.91 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 810 helix: 1.38 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -1.00 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1006 HIS 0.005 0.001 HIS A 782 PHE 0.011 0.001 PHE B 840 TYR 0.014 0.001 TYR A 780 ARG 0.004 0.000 ARG B1011 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 243 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7045 (mm-30) REVERT: B 971 ASN cc_start: 0.7645 (m110) cc_final: 0.7309 (m110) REVERT: B 1125 LYS cc_start: 0.7502 (tmmt) cc_final: 0.7269 (tmmt) outliers start: 26 outliers final: 24 residues processed: 252 average time/residue: 0.4611 time to fit residues: 150.9663 Evaluate side-chains 262 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 238 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 854 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 1008 SER Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1080 GLU Chi-restraints excluded: chain B residue 1095 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6874 Z= 0.237 Angle : 0.583 8.545 9307 Z= 0.314 Chirality : 0.036 0.155 1071 Planarity : 0.005 0.067 1175 Dihedral : 4.307 24.000 882 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.01 % Allowed : 32.43 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.92 (0.29), residues: 810 helix: 1.30 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -1.06 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1006 HIS 0.006 0.001 HIS A 782 PHE 0.011 0.001 PHE B 840 TYR 0.012 0.001 TYR A 780 ARG 0.008 0.000 ARG B1011 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 241 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7072 (mm-30) REVERT: B 971 ASN cc_start: 0.7703 (m110) cc_final: 0.7438 (m110) REVERT: B 1125 LYS cc_start: 0.7618 (tmmt) cc_final: 0.7382 (tmmt) outliers start: 31 outliers final: 28 residues processed: 252 average time/residue: 0.4966 time to fit residues: 161.4828 Evaluate side-chains 267 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 239 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 854 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 960 ASP Chi-restraints excluded: chain B residue 1008 SER Chi-restraints excluded: chain B residue 1055 ASP Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1080 GLU Chi-restraints excluded: chain B residue 1095 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0270 chunk 38 optimal weight: 0.3980 chunk 7 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6874 Z= 0.177 Angle : 0.566 6.736 9307 Z= 0.294 Chirality : 0.036 0.155 1071 Planarity : 0.005 0.061 1175 Dihedral : 4.124 25.249 882 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.58 % Allowed : 33.72 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.30), residues: 810 helix: 1.78 (0.22), residues: 574 sheet: None (None), residues: 0 loop : -0.86 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1006 HIS 0.005 0.001 HIS A 782 PHE 0.018 0.001 PHE B 754 TYR 0.022 0.001 TYR A 780 ARG 0.008 0.000 ARG B1011 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 241 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 GLU cc_start: 0.7644 (mm-30) cc_final: 0.6998 (mm-30) REVERT: B 967 ASN cc_start: 0.8478 (m110) cc_final: 0.8090 (m110) REVERT: B 971 ASN cc_start: 0.7608 (m110) cc_final: 0.7368 (m110) REVERT: B 998 TRP cc_start: 0.8614 (t-100) cc_final: 0.8183 (t-100) REVERT: B 1125 LYS cc_start: 0.7446 (tmmt) cc_final: 0.7210 (tmmt) outliers start: 20 outliers final: 16 residues processed: 248 average time/residue: 0.4784 time to fit residues: 152.5824 Evaluate side-chains 255 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 239 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1078 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6874 Z= 0.191 Angle : 0.575 6.649 9307 Z= 0.303 Chirality : 0.036 0.162 1071 Planarity : 0.004 0.060 1175 Dihedral : 4.090 24.950 882 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.33 % Allowed : 33.59 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.30), residues: 810 helix: 1.82 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -0.91 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1006 HIS 0.006 0.001 HIS A 782 PHE 0.011 0.001 PHE A 825 TYR 0.018 0.001 TYR A 780 ARG 0.007 0.000 ARG B1011 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 239 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7100 (mm-30) REVERT: B 971 ASN cc_start: 0.7624 (m110) cc_final: 0.7379 (m110) REVERT: B 998 TRP cc_start: 0.8627 (t-100) cc_final: 0.8226 (t-100) REVERT: B 1125 LYS cc_start: 0.7529 (tmmt) cc_final: 0.7295 (tmmt) outliers start: 18 outliers final: 17 residues processed: 244 average time/residue: 0.5005 time to fit residues: 157.9749 Evaluate side-chains 252 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 235 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1078 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6874 Z= 0.193 Angle : 0.587 7.114 9307 Z= 0.310 Chirality : 0.036 0.170 1071 Planarity : 0.004 0.059 1175 Dihedral : 4.058 25.013 882 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.45 % Allowed : 33.72 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.30), residues: 810 helix: 1.84 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -0.91 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1006 HIS 0.006 0.001 HIS A 782 PHE 0.012 0.001 PHE A 825 TYR 0.017 0.001 TYR A 780 ARG 0.007 0.000 ARG B1011 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 237 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7162 (mm-30) REVERT: B 971 ASN cc_start: 0.7635 (m110) cc_final: 0.7387 (m110) REVERT: B 998 TRP cc_start: 0.8627 (t-100) cc_final: 0.8229 (t-100) REVERT: B 1125 LYS cc_start: 0.7529 (tmmt) cc_final: 0.7297 (tmmt) outliers start: 19 outliers final: 19 residues processed: 242 average time/residue: 0.4856 time to fit residues: 153.1535 Evaluate side-chains 249 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 230 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 783 ASP Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1078 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 781 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.099265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.082258 restraints weight = 50548.929| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 4.64 r_work: 0.3397 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6874 Z= 0.190 Angle : 0.590 6.983 9307 Z= 0.310 Chirality : 0.036 0.164 1071 Planarity : 0.004 0.058 1175 Dihedral : 4.017 25.232 882 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.45 % Allowed : 34.50 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.30), residues: 810 helix: 1.87 (0.22), residues: 575 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1006 HIS 0.006 0.001 HIS A 782 PHE 0.016 0.001 PHE B 811 TYR 0.017 0.001 TYR A 780 ARG 0.008 0.000 ARG B1011 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4357.57 seconds wall clock time: 78 minutes 14.17 seconds (4694.17 seconds total)