Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 22:37:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5p_25706/04_2023/7t5p_25706.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5p_25706/04_2023/7t5p_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_2023/7t5p_25706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5p_25706/04_2023/7t5p_25706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5p_25706/04_2023/7t5p_25706.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5p_25706/04_2023/7t5p_25706.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 6.28, 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: 11.75 Conformation dependent library (CDL) restraints added in 1.1 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: 0.30 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: 5.25 Time building geometry restraints manager: 12.07 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: 4734 17.68 - 35.37: 612 35.37 - 53.05: 141 53.05 - 70.74: 27 70.74 - 88.42: 14 Dihedral angle restraints: 5528 sinusoidal: 2674 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 5525 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.210 Extract box with map and model: 3.030 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 45.510 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.270 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.266 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 outliers start: 3 outliers final: 3 residues processed: 246 average time/residue: 0.4362 time to fit residues: 139.8495 Evaluate side-chains 241 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 238 time to evaluate : 1.045 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1790 time to fit residues: 2.5293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 47 optimal weight: 0.0050 chunk 73 optimal weight: 0.9980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 952 GLN B1005 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.0717 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= 0.178 Angle : 0.554 5.960 9307 Z= 0.289 Chirality : 0.035 0.157 1071 Planarity : 0.004 0.054 1175 Dihedral : 4.002 15.800 880 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 1.42 % 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: 1.60 (0.30), residues: 810 helix: 1.89 (0.21), residues: 563 sheet: None (None), residues: 0 loop : -0.89 (0.41), residues: 247 *********************** 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 255 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 244 time to evaluate : 1.081 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 outliers start: 11 outliers final: 8 residues processed: 248 average time/residue: 0.4379 time to fit residues: 141.6021 Evaluate side-chains 240 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 232 time to evaluate : 1.085 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1582 time to fit residues: 3.6767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.7633 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 6874 Z= 0.335 Angle : 0.621 6.188 9307 Z= 0.348 Chirality : 0.037 0.156 1071 Planarity : 0.005 0.065 1175 Dihedral : 4.388 20.079 880 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 3.62 % 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: 0.57 (0.28), residues: 810 helix: 1.04 (0.20), residues: 573 sheet: None (None), residues: 0 loop : -1.19 (0.41), residues: 237 *********************** 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 263 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 235 time to evaluate : 1.148 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 outliers start: 28 outliers final: 26 residues processed: 248 average time/residue: 0.4634 time to fit residues: 150.1761 Evaluate side-chains 262 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 236 time to evaluate : 1.153 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.1684 time to fit residues: 9.2241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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** B1068 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 6874 Z= 0.246 Angle : 0.575 5.897 9307 Z= 0.313 Chirality : 0.036 0.158 1071 Planarity : 0.005 0.067 1175 Dihedral : 4.313 19.127 880 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 1.42 % 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: 0.68 (0.29), residues: 810 helix: 1.11 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -1.12 (0.41), residues: 235 *********************** 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 255 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 244 time to evaluate : 1.182 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 outliers start: 11 outliers final: 7 residues processed: 250 average time/residue: 0.4538 time to fit residues: 146.2970 Evaluate side-chains 242 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 235 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2311 time to fit residues: 3.9333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.0470 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- 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: 0.7606 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 6874 Z= 0.248 Angle : 0.575 5.862 9307 Z= 0.313 Chirality : 0.036 0.200 1071 Planarity : 0.005 0.067 1175 Dihedral : 4.298 19.324 880 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer Outliers : 1.42 % 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: 0.74 (0.29), residues: 810 helix: 1.17 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -1.14 (0.41), residues: 235 *********************** 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 249 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 238 time to evaluate : 1.143 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: 11 outliers final: 9 residues processed: 242 average time/residue: 0.4618 time to fit residues: 144.1128 Evaluate side-chains 240 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 231 time to evaluate : 1.148 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1607 time to fit residues: 4.0688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 0.7598 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 6874 Z= 0.234 Angle : 0.574 6.142 9307 Z= 0.310 Chirality : 0.036 0.156 1071 Planarity : 0.005 0.066 1175 Dihedral : 4.272 18.927 880 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 1.29 % 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: 0.83 (0.29), residues: 810 helix: 1.22 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -1.07 (0.42), residues: 235 *********************** 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 246 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 236 time to evaluate : 1.219 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: symmetry clash outliers start: 10 outliers final: 9 residues processed: 239 average time/residue: 0.4723 time to fit residues: 145.3062 Evaluate side-chains 246 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 237 time to evaluate : 1.127 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1588 time to fit residues: 4.0656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7560 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 6874 Z= 0.186 Angle : 0.565 9.239 9307 Z= 0.294 Chirality : 0.036 0.155 1071 Planarity : 0.004 0.062 1175 Dihedral : 4.086 16.944 880 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.90 % 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: 1.31 (0.30), residues: 810 helix: 1.59 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -0.91 (0.42), residues: 236 *********************** 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 246 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 239 time to evaluate : 1.049 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: 7 outliers final: 5 residues processed: 243 average time/residue: 0.4608 time to fit residues: 143.6389 Evaluate side-chains 240 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 235 time to evaluate : 1.123 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1532 time to fit residues: 2.9290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 7 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- 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: 0.7592 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 6874 Z= 0.236 Angle : 0.577 6.488 9307 Z= 0.310 Chirality : 0.036 0.154 1071 Planarity : 0.004 0.063 1175 Dihedral : 4.155 18.273 880 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer Outliers : 1.68 % 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: 1.12 (0.29), residues: 810 helix: 1.49 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -1.02 (0.41), residues: 242 *********************** 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 253 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 240 time to evaluate : 1.216 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: symmetry clash outliers start: 13 outliers final: 12 residues processed: 245 average time/residue: 0.4862 time to fit residues: 154.5911 Evaluate side-chains 248 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 236 time to evaluate : 1.067 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.1724 time to fit residues: 5.1879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 47 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7562 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 6874 Z= 0.191 Angle : 0.569 6.608 9307 Z= 0.299 Chirality : 0.036 0.155 1071 Planarity : 0.004 0.060 1175 Dihedral : 4.066 16.798 880 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.26 % 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: 1.37 (0.30), residues: 810 helix: 1.68 (0.21), residues: 569 sheet: None (None), residues: 0 loop : -0.94 (0.41), residues: 241 *********************** 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 243 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 241 time to evaluate : 1.255 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 outliers start: 2 outliers final: 2 residues processed: 243 average time/residue: 0.4651 time to fit residues: 145.3004 Evaluate side-chains 237 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 235 time to evaluate : 1.116 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.1796 time to fit residues: 2.0493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 51 optimal weight: 0.0970 chunk 68 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 6874 Z= 0.181 Angle : 0.571 6.842 9307 Z= 0.297 Chirality : 0.036 0.156 1071 Planarity : 0.004 0.058 1175 Dihedral : 3.939 15.129 880 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.65 % 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: 573 sheet: None (None), residues: 0 loop : -0.86 (0.42), residues: 237 ********************** 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 234 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 229 time to evaluate : 1.188 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 outliers start: 5 outliers final: 4 residues processed: 232 average time/residue: 0.4964 time to fit residues: 150.3146 Evaluate side-chains 237 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 233 time to evaluate : 1.114 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.1815 time to fit residues: 2.8057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.099143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.082150 restraints weight = 50662.374| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 4.56 r_work: 0.3396 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 6874 Z= 0.190 Angle : 0.578 6.972 9307 Z= 0.303 Chirality : 0.036 0.161 1071 Planarity : 0.004 0.058 1175 Dihedral : 3.928 15.454 880 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.26 % 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 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -0.87 (0.41), residues: 242 =============================================================================== Job complete usr+sys time: 4061.19 seconds wall clock time: 72 minutes 17.00 seconds (4337.00 seconds total)