Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 17:44:16 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n72_24217/12_2021/7n72_24217_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n72_24217/12_2021/7n72_24217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n72_24217/12_2021/7n72_24217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n72_24217/12_2021/7n72_24217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n72_24217/12_2021/7n72_24217_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n72_24217/12_2021/7n72_24217_trim_updated.pdb" } resolution = 2.5 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 PHE 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 7705 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1046, 7705 Unusual residues: {' MG': 1, 'ALF': 1, 'PC1': 2, 'LMT': 3, 'Y01': 3, 'SPM': 1} Classifications: {'undetermined': 11, 'water': 5, 'peptide': 1030} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 68, 'TRANS': 958, None: 16, 'PCIS': 3} Not linked: pdbres="PRO A1168 " pdbres="ALF A1201 " Not linked: pdbres="ALF A1201 " pdbres=" MG A1202 " Not linked: pdbres=" MG A1202 " pdbres="SPM A1203 " Not linked: pdbres="SPM A1203 " pdbres="Y01 A1204 " Not linked: pdbres="Y01 A1204 " pdbres="Y01 A1205 " ... (remaining 11 not shown) Chain breaks: 6 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 623 Unresolved non-hydrogen angles: 811 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 6, 'HIS:plan': 2, 'PC1:plan-2': 1, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 294 Time building chain proxies: 5.00, per 1000 atoms: 0.65 Number of scatterers: 7705 At special positions: 0 Unit cell: (80.773, 104.9, 135.321, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 46 16.00 P 1 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1364 8.00 N 1287 7.00 C 5001 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 Amimo 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.1 seconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 9 sheets defined 46.6% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.640A pdb=" N SER A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N HIS A 197 " --> pdb=" O HIS A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 211 Processing helix chain 'A' and resid 223 through 230 removed outlier: 4.068A pdb=" N ASP A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 248 Processing helix chain 'A' and resid 252 through 284 Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 338 through 341 No H-bonds generated for 'chain 'A' and resid 338 through 341' Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 398 through 407 Processing helix chain 'A' and resid 417 through 444 Processing helix chain 'A' and resid 449 through 463 removed outlier: 3.728A pdb=" N VAL A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 486 removed outlier: 4.322A pdb=" N CYS A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR A 476 " --> pdb=" O MET A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 545 through 552 Processing helix chain 'A' and resid 567 through 576 Processing helix chain 'A' and resid 652 through 655 No H-bonds generated for 'chain 'A' and resid 652 through 655' Processing helix chain 'A' and resid 668 through 678 removed outlier: 4.397A pdb=" N ALA A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 699 No H-bonds generated for 'chain 'A' and resid 696 through 699' Processing helix chain 'A' and resid 704 through 708 Processing helix chain 'A' and resid 727 through 736 Processing helix chain 'A' and resid 749 through 758 Processing helix chain 'A' and resid 822 through 831 Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 851 through 863 Processing helix chain 'A' and resid 875 through 883 removed outlier: 4.853A pdb=" N GLY A 879 " --> pdb=" O ASN A 876 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 883 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 949 Proline residue: A 912 - end of helix removed outlier: 3.548A pdb=" N THR A 938 " --> pdb=" O TYR A 935 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A 939 " --> pdb=" O SER A 936 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 948 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 973 removed outlier: 3.967A pdb=" N ILE A 965 " --> pdb=" O ILE A 961 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR A 966 " --> pdb=" O ASP A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1018 Processing helix chain 'A' and resid 1040 through 1060 removed outlier: 3.787A pdb=" N PHE A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1072 No H-bonds generated for 'chain 'A' and resid 1070 through 1072' Processing helix chain 'A' and resid 1074 through 1092 Processing helix chain 'A' and resid 1109 through 1144 Proline residue: A1138 - end of helix Processing helix chain 'A' and resid 1153 through 1163 Processing sheet with id= A, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.655A pdb=" N GLU A 91 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN A 101 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 160 through 163 Processing sheet with id= C, first strand: chain 'A' and resid 298 through 303 removed outlier: 4.539A pdb=" N CYS A 291 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N CYS A 312 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL A 386 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP A 325 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.133A pdb=" N ASN A 336 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE A 375 " --> pdb=" O ASN A 336 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 488 through 490 Processing sheet with id= F, first strand: chain 'A' and resid 740 through 743 removed outlier: 6.473A pdb=" N VAL A 886 " --> pdb=" O MET A 870 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY A 872 " --> pdb=" O VAL A 886 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE A 888 " --> pdb=" O GLY A 872 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 557 through 559 Processing sheet with id= H, first strand: chain 'A' and resid 588 through 590 removed outlier: 3.925A pdb=" N SER A 588 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 635 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ARG A 622 " --> pdb=" O SER A 633 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER A 633 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER A 687 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU A 713 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG A 720 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL A 520 " --> pdb=" O ARG A 720 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 783 through 789 removed outlier: 3.692A pdb=" N SER A 783 " --> pdb=" O THR A 774 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU A 768 " --> pdb=" O MET A 789 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER A 821 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ALA A 773 " --> pdb=" O SER A 821 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU A 820 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE A 846 " --> pdb=" O LEU A 820 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1044 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: 2.94 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1975 1.33 - 1.45: 1232 1.45 - 1.57: 4560 1.57 - 1.69: 12 1.69 - 1.81: 72 Bond restraints: 7851 Sorted by residual: bond pdb=" C31 PC1 A1206 " pdb=" O31 PC1 A1206 " ideal model delta sigma weight residual 1.330 1.456 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C21 PC1 A1210 " pdb=" O21 PC1 A1210 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C21 PC1 A1206 " pdb=" O21 PC1 A1206 " ideal model delta sigma weight residual 1.331 1.452 -0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" CAY Y01 A1211 " pdb=" OAW Y01 A1211 " ideal model delta sigma weight residual 1.332 1.412 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CAY Y01 A1204 " pdb=" OAW Y01 A1204 " ideal model delta sigma weight residual 1.332 1.409 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 7846 not shown) Histogram of bond angle deviations from ideal: 87.16 - 105.12: 231 105.12 - 123.09: 10062 123.09 - 141.06: 416 141.06 - 159.03: 0 159.03 - 177.00: 2 Bond angle restraints: 10711 Sorted by residual: angle pdb=" CAM Y01 A1211 " pdb=" CAY Y01 A1211 " pdb=" OAW Y01 A1211 " ideal model delta sigma weight residual 111.19 125.78 -14.59 3.00e+00 1.11e-01 2.37e+01 angle pdb=" CAM Y01 A1204 " pdb=" CAY Y01 A1204 " pdb=" OAW Y01 A1204 " ideal model delta sigma weight residual 111.19 125.75 -14.56 3.00e+00 1.11e-01 2.36e+01 angle pdb=" CAM Y01 A1205 " pdb=" CAY Y01 A1205 " pdb=" OAW Y01 A1205 " ideal model delta sigma weight residual 111.19 125.54 -14.35 3.00e+00 1.11e-01 2.29e+01 angle pdb=" CA LEU A 787 " pdb=" CB LEU A 787 " pdb=" CG LEU A 787 " ideal model delta sigma weight residual 116.30 129.70 -13.40 3.50e+00 8.16e-02 1.47e+01 angle pdb=" C ILE A 60 " pdb=" CA ILE A 60 " pdb=" CB ILE A 60 " ideal model delta sigma weight residual 114.35 111.11 3.24 1.06e+00 8.90e-01 9.37e+00 ... (remaining 10706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4326 17.81 - 35.62: 301 35.62 - 53.43: 50 53.43 - 71.24: 11 71.24 - 89.05: 6 Dihedral angle restraints: 4694 sinusoidal: 1720 harmonic: 2974 Sorted by residual: dihedral pdb=" CA PRO A1026 " pdb=" C PRO A1026 " pdb=" N LEU A1027 " pdb=" CA LEU A1027 " ideal model delta harmonic sigma weight residual -180.00 -157.82 -22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA PHE A 507 " pdb=" C PHE A 507 " pdb=" N ASP A 508 " pdb=" CA ASP A 508 " ideal model delta harmonic sigma weight residual 180.00 160.14 19.86 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA TYR A 251 " pdb=" C TYR A 251 " pdb=" N TYR A 252 " pdb=" CA TYR A 252 " ideal model delta harmonic sigma weight residual -180.00 -161.27 -18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 4691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1131 0.076 - 0.151: 155 0.151 - 0.227: 11 0.227 - 0.302: 2 0.302 - 0.378: 7 Chirality restraints: 1306 Sorted by residual: chirality pdb=" CBG Y01 A1211 " pdb=" CAQ Y01 A1211 " pdb=" CBD Y01 A1211 " pdb=" CBI Y01 A1211 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CBG Y01 A1204 " pdb=" CAQ Y01 A1204 " pdb=" CBD Y01 A1204 " pdb=" CBI Y01 A1204 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CBG Y01 A1205 " pdb=" CAQ Y01 A1205 " pdb=" CBD Y01 A1205 " pdb=" CBI Y01 A1205 " both_signs ideal model delta sigma weight residual False -2.33 -2.70 0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 1303 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 202 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" CD GLN A 202 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLN A 202 " 0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN A 202 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 164 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" CD GLN A 164 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLN A 164 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN A 164 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A1135 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" CD GLN A1135 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLN A1135 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN A1135 " 0.011 2.00e-02 2.50e+03 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 47 2.56 - 3.14: 6007 3.14 - 3.73: 12144 3.73 - 4.31: 17386 4.31 - 4.90: 28968 Nonbonded interactions: 64552 Sorted by model distance: nonbonded pdb=" F2 ALF A1201 " pdb="MG MG A1202 " model vdw 1.971 2.120 nonbonded pdb=" OD2 ASP A 458 " pdb=" O HOH A1301 " model vdw 2.023 2.440 nonbonded pdb=" OD2 ASP A 508 " pdb="MG MG A1202 " model vdw 2.105 2.170 nonbonded pdb=" O THR A 510 " pdb="MG MG A1202 " model vdw 2.211 2.170 nonbonded pdb=" N1 SPM A1203 " pdb=" O HOH A1302 " model vdw 2.234 2.520 ... (remaining 64547 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 1 5.49 5 Mg 1 5.21 5 S 46 5.16 5 C 5001 2.51 5 N 1287 2.21 5 O 1364 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 individual isotropic Write .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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.350 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.080 Process input model: 24.550 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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:12.010 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 44.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 : 0.007 0.126 7851 Z= 0.441 Angle : 0.870 14.592 10711 Z= 0.396 Chirality : 0.058 0.378 1306 Planarity : 0.006 0.043 1335 Dihedral : 13.123 89.046 2772 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.87 (0.24), residues: 1016 helix: -0.20 (0.21), residues: 484 sheet: -0.59 (0.38), residues: 163 loop : -0.87 (0.31), residues: 369 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.827 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 1.1751 time to fit residues: 99.2604 Evaluate side-chains 49 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 0.2980 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 40.0000 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 7851 Z= 0.192 Angle : 0.543 8.512 10711 Z= 0.271 Chirality : 0.041 0.145 1306 Planarity : 0.006 0.051 1335 Dihedral : 7.928 59.648 1209 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1016 helix: 0.98 (0.23), residues: 486 sheet: -0.15 (0.38), residues: 165 loop : -0.17 (0.33), residues: 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.930 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 54 average time/residue: 0.9489 time to fit residues: 56.2706 Evaluate side-chains 47 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 94 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7851 Z= 0.164 Angle : 0.507 8.132 10711 Z= 0.251 Chirality : 0.040 0.152 1306 Planarity : 0.005 0.043 1335 Dihedral : 7.293 56.883 1209 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 0.91 (0.27), residues: 1016 helix: 1.34 (0.24), residues: 485 sheet: -0.16 (0.36), residues: 175 loop : 0.17 (0.35), residues: 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.875 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 56 average time/residue: 0.8718 time to fit residues: 53.8996 Evaluate side-chains 46 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1370 time to fit residues: 1.3777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 27 optimal weight: 0.3980 chunk 83 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN A 179 GLN A 385 HIS ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 : 0.003 0.024 7851 Z= 0.168 Angle : 0.501 8.361 10711 Z= 0.246 Chirality : 0.040 0.144 1306 Planarity : 0.005 0.043 1335 Dihedral : 6.852 55.876 1209 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.24 (0.27), residues: 1016 helix: 1.56 (0.24), residues: 486 sheet: 0.04 (0.37), residues: 175 loop : 0.38 (0.35), residues: 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.870 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 51 average time/residue: 0.9305 time to fit residues: 52.2283 Evaluate side-chains 44 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1417 time to fit residues: 1.4566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 50.0000 chunk 1 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 90 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 7851 Z= 0.210 Angle : 0.513 8.874 10711 Z= 0.251 Chirality : 0.040 0.142 1306 Planarity : 0.005 0.043 1335 Dihedral : 6.621 56.992 1209 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.36 (0.27), residues: 1016 helix: 1.62 (0.24), residues: 486 sheet: 0.25 (0.37), residues: 174 loop : 0.42 (0.35), residues: 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.937 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 57 average time/residue: 0.8003 time to fit residues: 50.7972 Evaluate side-chains 47 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1272 time to fit residues: 1.4448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 59 optimal weight: 30.0000 chunk 24 optimal weight: 3.9990 chunk 100 optimal weight: 0.0070 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 30.0000 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 179 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 7851 Z= 0.173 Angle : 0.495 9.138 10711 Z= 0.244 Chirality : 0.040 0.139 1306 Planarity : 0.006 0.106 1335 Dihedral : 6.438 58.712 1209 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.51 (0.27), residues: 1016 helix: 1.74 (0.24), residues: 483 sheet: 0.34 (0.37), residues: 174 loop : 0.49 (0.35), residues: 359 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.891 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 0.8307 time to fit residues: 48.0807 Evaluate side-chains 48 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.1407 time to fit residues: 1.4436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.0770 chunk 57 optimal weight: 0.0980 chunk 73 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 100 optimal weight: 0.0370 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 30.0000 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.324 7851 Z= 0.332 Angle : 0.642 27.428 10711 Z= 0.341 Chirality : 0.040 0.128 1306 Planarity : 0.006 0.097 1335 Dihedral : 6.315 59.504 1209 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.27), residues: 1016 helix: 1.80 (0.24), residues: 483 sheet: 0.44 (0.37), residues: 174 loop : 0.49 (0.35), residues: 359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.889 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 53 average time/residue: 0.9074 time to fit residues: 53.2986 Evaluate side-chains 49 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1426 time to fit residues: 1.6492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 40.0000 chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 7851 Z= 0.214 Angle : 0.575 14.087 10711 Z= 0.281 Chirality : 0.040 0.148 1306 Planarity : 0.005 0.093 1335 Dihedral : 6.357 59.459 1209 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.61 (0.27), residues: 1016 helix: 1.80 (0.24), residues: 484 sheet: 0.48 (0.37), residues: 174 loop : 0.50 (0.34), residues: 358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.896 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.9110 time to fit residues: 49.3998 Evaluate side-chains 49 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1401 time to fit residues: 1.6891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.0970 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 0.0030 chunk 88 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 7851 Z= 0.165 Angle : 0.536 12.551 10711 Z= 0.260 Chirality : 0.039 0.132 1306 Planarity : 0.005 0.090 1335 Dihedral : 6.201 59.847 1209 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.69 (0.27), residues: 1016 helix: 1.90 (0.24), residues: 484 sheet: 0.57 (0.38), residues: 173 loop : 0.47 (0.35), residues: 359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.949 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 0.8871 time to fit residues: 51.0319 Evaluate side-chains 49 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.832 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.1448 time to fit residues: 1.4446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 30.0000 chunk 68 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 7851 Z= 0.199 Angle : 0.549 11.968 10711 Z= 0.266 Chirality : 0.040 0.133 1306 Planarity : 0.005 0.095 1335 Dihedral : 6.189 59.432 1209 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.68 (0.27), residues: 1016 helix: 1.87 (0.24), residues: 485 sheet: 0.55 (0.38), residues: 172 loop : 0.50 (0.35), residues: 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.881 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 52 average time/residue: 0.8826 time to fit residues: 50.8106 Evaluate side-chains 50 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.1394 time to fit residues: 1.4473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.108450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.074043 restraints weight = 12729.470| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.14 r_work: 0.2990 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work: 0.2969 rms_B_bonded: 1.97 restraints_weight: 0.1250 r_work: 0.2958 rms_B_bonded: 2.01 restraints_weight: 0.0625 r_work: 0.2948 rms_B_bonded: 2.07 restraints_weight: 0.0312 r_work: 0.2936 rms_B_bonded: 2.15 restraints_weight: 0.0156 r_work: 0.2925 rms_B_bonded: 2.25 restraints_weight: 0.0078 r_work: 0.2913 rms_B_bonded: 2.36 restraints_weight: 0.0039 r_work: 0.2901 rms_B_bonded: 2.49 restraints_weight: 0.0020 r_work: 0.2888 rms_B_bonded: 2.64 restraints_weight: 0.0010 r_work: 0.2874 rms_B_bonded: 2.81 restraints_weight: 0.0005 r_work: 0.2860 rms_B_bonded: 3.00 restraints_weight: 0.0002 r_work: 0.2846 rms_B_bonded: 3.21 restraints_weight: 0.0001 r_work: 0.2830 rms_B_bonded: 3.44 restraints_weight: 0.0001 r_work: 0.2814 rms_B_bonded: 3.70 restraints_weight: 0.0000 r_work: 0.2797 rms_B_bonded: 3.98 restraints_weight: 0.0000 r_work: 0.2779 rms_B_bonded: 4.30 restraints_weight: 0.0000 r_work: 0.2760 rms_B_bonded: 4.64 restraints_weight: 0.0000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 7851 Z= 0.259 Angle : 0.574 11.240 10711 Z= 0.279 Chirality : 0.041 0.159 1306 Planarity : 0.005 0.097 1335 Dihedral : 6.440 59.288 1209 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.61 (0.27), residues: 1016 helix: 1.77 (0.24), residues: 485 sheet: 0.63 (0.38), residues: 171 loop : 0.47 (0.35), residues: 360 =============================================================================== Job complete usr+sys time: 2029.38 seconds wall clock time: 37 minutes 14.07 seconds (2234.07 seconds total)