Starting phenix.real_space_refine (version: dev) on Thu May 12 22:59:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op1_13011/05_2022/7op1_13011_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op1_13011/05_2022/7op1_13011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op1_13011/05_2022/7op1_13011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op1_13011/05_2022/7op1_13011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op1_13011/05_2022/7op1_13011_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op1_13011/05_2022/7op1_13011_updated.pdb" } resolution = 3.7 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= 0.001 sd= 0.054 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 8744 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8744 Unusual residues: {'ALF': 1, ' MG': 1, 'SPM': 1} Classifications: {'undetermined': 3, 'peptide': 1098} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1043, None: 3} Not linked: pdbres="PHE A1393 " pdbres=" MG A1401 " Not linked: pdbres=" MG A1401 " pdbres="ALF A1402 " Not linked: pdbres="ALF A1402 " pdbres="SPM A1403 " Chain breaks: 7 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.94, per 1000 atoms: 0.68 Number of scatterers: 8744 At special positions: 0 Unit cell: (86.17, 101.681, 143.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 53 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1550 8.00 N 1452 7.00 C 5683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 4.10 Conformation dependent library (CDL) restraints added in 1.5 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 10 sheets defined 43.6% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 229 through 240 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 362 through 372 removed outlier: 3.831A pdb=" N HIS A 367 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE A 372 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 395 through 410 Processing helix chain 'A' and resid 413 through 441 Processing helix chain 'A' and resid 517 through 520 No H-bonds generated for 'chain 'A' and resid 517 through 520' Processing helix chain 'A' and resid 530 through 535 removed outlier: 5.027A pdb=" N HIS A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 570 through 578 Processing helix chain 'A' and resid 589 through 616 removed outlier: 3.787A pdb=" N LEU A 605 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 635 removed outlier: 3.980A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 657 removed outlier: 4.059A pdb=" N GLN A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 654 " --> pdb=" O PHE A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 673 removed outlier: 4.014A pdb=" N ASN A 669 " --> pdb=" O GLN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 716 No H-bonds generated for 'chain 'A' and resid 713 through 716' Processing helix chain 'A' and resid 749 through 759 Processing helix chain 'A' and resid 774 through 783 removed outlier: 3.736A pdb=" N LYS A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 868 No H-bonds generated for 'chain 'A' and resid 865 through 868' Processing helix chain 'A' and resid 881 through 891 Processing helix chain 'A' and resid 910 through 913 No H-bonds generated for 'chain 'A' and resid 910 through 913' Processing helix chain 'A' and resid 916 through 920 Processing helix chain 'A' and resid 939 through 948 removed outlier: 3.682A pdb=" N LYS A 944 " --> pdb=" O THR A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 1044 through 1052 removed outlier: 3.810A pdb=" N TRP A1048 " --> pdb=" O ASP A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1064 Processing helix chain 'A' and resid 1073 through 1086 removed outlier: 3.835A pdb=" N ILE A1086 " --> pdb=" O LYS A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1105 removed outlier: 4.881A pdb=" N ALA A1101 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A1105 " --> pdb=" O ALA A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1171 removed outlier: 3.947A pdb=" N VAL A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N SER A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1186 Processing helix chain 'A' and resid 1188 through 1196 removed outlier: 3.811A pdb=" N SER A1196 " --> pdb=" O ALA A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1242 Proline residue: A1221 - end of helix removed outlier: 3.642A pdb=" N SER A1224 " --> pdb=" O VAL A1220 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS A1225 " --> pdb=" O PRO A1221 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN A1242 " --> pdb=" O VAL A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1280 removed outlier: 3.844A pdb=" N ILE A1275 " --> pdb=" O CYS A1271 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A1276 " --> pdb=" O PHE A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1293 No H-bonds generated for 'chain 'A' and resid 1291 through 1293' Processing helix chain 'A' and resid 1295 through 1313 Processing helix chain 'A' and resid 1317 through 1320 No H-bonds generated for 'chain 'A' and resid 1317 through 1320' Processing helix chain 'A' and resid 1330 through 1352 removed outlier: 4.030A pdb=" N ILE A1334 " --> pdb=" O TRP A1330 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A1335 " --> pdb=" O THR A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1370 Processing helix chain 'A' and resid 1378 through 1392 Processing sheet with id= A, first strand: chain 'A' and resid 206 through 210 removed outlier: 3.947A pdb=" N TRP A 270 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 223 through 225 Processing sheet with id= C, first strand: chain 'A' and resid 322 through 325 Processing sheet with id= D, first strand: chain 'A' and resid 450 through 453 Processing sheet with id= E, first strand: chain 'A' and resid 472 through 474 removed outlier: 7.241A pdb=" N ASP A 486 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 508 through 511 removed outlier: 7.029A pdb=" N ASN A 497 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU A 543 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 695 through 697 removed outlier: 6.649A pdb=" N CYS A 898 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE A 928 " --> pdb=" O ILE A 896 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE A 896 " --> pdb=" O PHE A 928 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE A 930 " --> pdb=" O ARG A 894 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG A 894 " --> pdb=" O ILE A 930 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ARG A 850 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL A 832 " --> pdb=" O ARG A 850 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 764 through 766 Processing sheet with id= I, first strand: chain 'A' and resid 981 through 985 Processing sheet with id= J, first strand: chain 'A' and resid 1091 through 1094 removed outlier: 6.965A pdb=" N VAL A1108 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N GLY A1094 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE A1110 " --> pdb=" O GLY A1094 " (cutoff:3.500A) No H-bonds generated for sheet with id= J 356 hydrogen bonds defined for protein. 999 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: 3.40 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2717 1.34 - 1.46: 1444 1.46 - 1.57: 4714 1.57 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 8956 Sorted by residual: bond pdb=" F1 ALF A1402 " pdb="AL ALF A1402 " ideal model delta sigma weight residual 1.684 1.783 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" F3 ALF A1402 " pdb="AL ALF A1402 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" F2 ALF A1402 " pdb="AL ALF A1402 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" F4 ALF A1402 " pdb="AL ALF A1402 " ideal model delta sigma weight residual 1.686 1.783 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" CG GLN A 653 " pdb=" CD GLN A 653 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.12e+00 ... (remaining 8951 not shown) Histogram of bond angle deviations from ideal: 89.03 - 107.17: 289 107.17 - 125.31: 11714 125.31 - 143.44: 154 143.44 - 161.58: 0 161.58 - 179.72: 2 Bond angle restraints: 12159 Sorted by residual: angle pdb=" F1 ALF A1402 " pdb="AL ALF A1402 " pdb=" F2 ALF A1402 " ideal model delta sigma weight residual 108.68 179.72 -71.04 3.00e+00 1.11e-01 5.61e+02 angle pdb=" F3 ALF A1402 " pdb="AL ALF A1402 " pdb=" F4 ALF A1402 " ideal model delta sigma weight residual 109.63 179.59 -69.96 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F2 ALF A1402 " pdb="AL ALF A1402 " pdb=" F3 ALF A1402 " ideal model delta sigma weight residual 109.59 89.03 20.56 3.00e+00 1.11e-01 4.70e+01 angle pdb=" F1 ALF A1402 " pdb="AL ALF A1402 " pdb=" F4 ALF A1402 " ideal model delta sigma weight residual 109.02 89.10 19.92 3.00e+00 1.11e-01 4.41e+01 angle pdb=" F2 ALF A1402 " pdb="AL ALF A1402 " pdb=" F4 ALF A1402 " ideal model delta sigma weight residual 110.21 90.77 19.44 3.00e+00 1.11e-01 4.20e+01 ... (remaining 12154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 4766 17.45 - 34.89: 463 34.89 - 52.34: 68 52.34 - 69.78: 10 69.78 - 87.23: 6 Dihedral angle restraints: 5313 sinusoidal: 2103 harmonic: 3210 Sorted by residual: dihedral pdb=" CA TYR A 327 " pdb=" C TYR A 327 " pdb=" N TYR A 328 " pdb=" CA TYR A 328 " ideal model delta harmonic sigma weight residual 180.00 161.45 18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA TYR A 413 " pdb=" C TYR A 413 " pdb=" N TYR A 414 " pdb=" CA TYR A 414 " ideal model delta harmonic sigma weight residual -180.00 -162.26 -17.74 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASP A 347 " pdb=" C ASP A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta harmonic sigma weight residual 180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 768 0.029 - 0.059: 403 0.059 - 0.088: 120 0.088 - 0.117: 76 0.117 - 0.147: 20 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA PRO A 348 " pdb=" N PRO A 348 " pdb=" C PRO A 348 " pdb=" CB PRO A 348 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA VAL A 580 " pdb=" N VAL A 580 " pdb=" C VAL A 580 " pdb=" CB VAL A 580 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE A 495 " pdb=" N ILE A 495 " pdb=" C ILE A 495 " pdb=" CB ILE A 495 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1384 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 347 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" CG ASP A 347 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP A 347 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP A 347 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 982 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 983 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 983 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 983 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 877 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 878 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 878 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 878 " 0.026 5.00e-02 4.00e+02 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 34 2.46 - 3.07: 5769 3.07 - 3.68: 12313 3.68 - 4.29: 17685 4.29 - 4.90: 30056 Nonbonded interactions: 65857 Sorted by model distance: nonbonded pdb="MG MG A1401 " pdb=" F3 ALF A1402 " model vdw 1.848 2.120 nonbonded pdb="MG MG A1401 " pdb=" F2 ALF A1402 " model vdw 1.971 2.120 nonbonded pdb=" OD2 ASP A 680 " pdb=" F2 ALF A1402 " model vdw 2.069 2.390 nonbonded pdb=" OD2 ASP A 680 " pdb="MG MG A1401 " model vdw 2.081 2.170 nonbonded pdb=" OG SER A1290 " pdb=" OE1 GLU A1293 " model vdw 2.135 2.440 ... (remaining 65852 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 53 5.16 5 C 5683 2.51 5 N 1452 2.21 5 O 1550 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.000 Extract box with map and model: 7.480 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 30.070 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 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 : 0.004 0.099 8956 Z= 0.276 Angle : 1.157 71.036 12159 Z= 0.482 Chirality : 0.043 0.147 1387 Planarity : 0.004 0.048 1516 Dihedral : 13.672 87.230 3235 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.26), residues: 1082 helix: 0.90 (0.24), residues: 485 sheet: -1.18 (0.51), residues: 114 loop : -1.71 (0.27), residues: 483 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.031 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1841 time to fit residues: 23.4817 Evaluate side-chains 68 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.160 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 0.0050 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 8956 Z= 0.145 Angle : 0.499 6.889 12159 Z= 0.260 Chirality : 0.040 0.152 1387 Planarity : 0.004 0.094 1516 Dihedral : 5.503 58.836 1206 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.27), residues: 1082 helix: 1.44 (0.25), residues: 486 sheet: -1.06 (0.45), residues: 141 loop : -1.39 (0.30), residues: 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 1.020 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 81 average time/residue: 0.1878 time to fit residues: 22.6425 Evaluate side-chains 78 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0826 time to fit residues: 2.3244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.0770 chunk 31 optimal weight: 0.0000 chunk 83 optimal weight: 0.0770 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.3300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 8956 Z= 0.120 Angle : 0.474 9.458 12159 Z= 0.243 Chirality : 0.039 0.144 1387 Planarity : 0.004 0.097 1516 Dihedral : 5.066 57.600 1206 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.27), residues: 1082 helix: 1.66 (0.25), residues: 487 sheet: -0.94 (0.44), residues: 151 loop : -1.30 (0.30), residues: 444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1899 time to fit residues: 23.5100 Evaluate side-chains 67 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 0.0370 chunk 47 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 8956 Z= 0.157 Angle : 0.472 5.910 12159 Z= 0.247 Chirality : 0.040 0.141 1387 Planarity : 0.004 0.091 1516 Dihedral : 4.950 57.760 1206 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.27), residues: 1082 helix: 1.71 (0.25), residues: 483 sheet: -0.76 (0.45), residues: 151 loop : -1.20 (0.30), residues: 448 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 1.087 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 74 average time/residue: 0.2047 time to fit residues: 22.8720 Evaluate side-chains 75 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1282 time to fit residues: 3.2349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 0.0040 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 0.0170 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 30.0000 chunk 95 optimal weight: 0.2980 chunk 26 optimal weight: 0.4980 overall best weight: 0.3632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 8956 Z= 0.121 Angle : 0.449 5.774 12159 Z= 0.235 Chirality : 0.039 0.139 1387 Planarity : 0.004 0.108 1516 Dihedral : 4.667 58.074 1206 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.27), residues: 1082 helix: 1.92 (0.25), residues: 481 sheet: -0.50 (0.47), residues: 146 loop : -1.14 (0.30), residues: 455 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 1.014 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 81 average time/residue: 0.1914 time to fit residues: 23.0256 Evaluate side-chains 71 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 chunk 102 optimal weight: 0.3980 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN A1352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.046 8956 Z= 0.446 Angle : 0.622 7.007 12159 Z= 0.325 Chirality : 0.046 0.143 1387 Planarity : 0.004 0.078 1516 Dihedral : 5.575 58.177 1206 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1082 helix: 1.21 (0.24), residues: 486 sheet: -0.85 (0.49), residues: 128 loop : -1.36 (0.29), residues: 468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 1.019 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 83 average time/residue: 0.1988 time to fit residues: 24.3334 Evaluate side-chains 77 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0821 time to fit residues: 2.6606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.191 8956 Z= 0.199 Angle : 0.530 13.996 12159 Z= 0.279 Chirality : 0.041 0.140 1387 Planarity : 0.004 0.062 1516 Dihedral : 5.042 56.900 1206 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 1082 helix: 1.65 (0.25), residues: 473 sheet: -0.70 (0.44), residues: 151 loop : -1.13 (0.30), residues: 458 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 1.072 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 79 average time/residue: 0.1989 time to fit residues: 23.4883 Evaluate side-chains 74 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0855 time to fit residues: 2.1211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.0970 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.127 8956 Z= 0.177 Angle : 0.490 8.840 12159 Z= 0.256 Chirality : 0.040 0.159 1387 Planarity : 0.004 0.090 1516 Dihedral : 4.751 59.616 1206 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.27), residues: 1082 helix: 1.82 (0.25), residues: 474 sheet: -0.49 (0.45), residues: 151 loop : -1.18 (0.30), residues: 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.932 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 76 average time/residue: 0.2096 time to fit residues: 23.2522 Evaluate side-chains 73 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.944 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0944 time to fit residues: 1.4359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.0050 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 64 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.099 8956 Z= 0.161 Angle : 0.474 6.346 12159 Z= 0.245 Chirality : 0.040 0.146 1387 Planarity : 0.004 0.065 1516 Dihedral : 4.532 59.575 1206 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 1082 helix: 1.83 (0.25), residues: 481 sheet: -0.43 (0.44), residues: 153 loop : -1.15 (0.30), residues: 448 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.146 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1809 time to fit residues: 19.6523 Evaluate side-chains 69 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 6.9990 chunk 72 optimal weight: 0.0970 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 0.0030 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 overall best weight: 0.2966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.091 8956 Z= 0.141 Angle : 0.478 8.169 12159 Z= 0.244 Chirality : 0.039 0.141 1387 Planarity : 0.004 0.053 1516 Dihedral : 4.294 58.613 1206 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.27), residues: 1082 helix: 1.98 (0.25), residues: 481 sheet: -0.23 (0.45), residues: 149 loop : -1.06 (0.30), residues: 452 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.053 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2007 time to fit residues: 22.9518 Evaluate side-chains 72 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.156066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.122588 restraints weight = 11643.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119548 restraints weight = 14752.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.120600 restraints weight = 15581.929| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 8956 Z= 0.200 Angle : 0.510 7.546 12159 Z= 0.260 Chirality : 0.040 0.140 1387 Planarity : 0.004 0.050 1516 Dihedral : 4.460 55.933 1206 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.27), residues: 1082 helix: 1.86 (0.25), residues: 481 sheet: -0.33 (0.44), residues: 154 loop : -1.09 (0.30), residues: 447 =============================================================================== Job complete usr+sys time: 1654.01 seconds wall clock time: 30 minutes 48.82 seconds (1848.82 seconds total)