Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 02:17:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmu_22264/10_2023/6xmu_22264_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmu_22264/10_2023/6xmu_22264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmu_22264/10_2023/6xmu_22264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmu_22264/10_2023/6xmu_22264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmu_22264/10_2023/6xmu_22264_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmu_22264/10_2023/6xmu_22264_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 38 5.16 5 Be 1 3.05 5 C 5422 2.51 5 N 1398 2.21 5 O 1548 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 175": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A ARG 480": "NH1" <-> "NH2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ARG 588": "NH1" <-> "NH2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 630": "NH1" <-> "NH2" Residue "A ARG 656": "NH1" <-> "NH2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A GLU 838": "OE1" <-> "OE2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A GLU 1128": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 8411 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8306 Classifications: {'peptide': 1090} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 49, 'TRANS': 1040} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 176 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.68, per 1000 atoms: 0.56 Number of scatterers: 8411 At special positions: 0 Unit cell: (91.63, 88.06, 145.18, 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 38 16.00 Mg 1 11.99 F 3 9.00 O 1548 8.00 N 1398 7.00 C 5422 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.6 seconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 8 sheets defined 42.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 27 through 43 Proline residue: A 31 - end of helix Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 58 through 73 Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 173 through 176 No H-bonds generated for 'chain 'A' and resid 173 through 176' Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.215A pdb=" N GLU A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 213 Processing helix chain 'A' and resid 219 through 246 Processing helix chain 'A' and resid 333 through 336 removed outlier: 4.322A pdb=" N ILE A 336 " --> pdb=" O VAL A 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 397 through 424 Processing helix chain 'A' and resid 428 through 441 Processing helix chain 'A' and resid 447 through 465 removed outlier: 3.985A pdb=" N LYS A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 476 through 479 removed outlier: 3.531A pdb=" N GLY A 479 " --> pdb=" O PRO A 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 476 through 479' Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.790A pdb=" N GLY A 530 " --> pdb=" O ILE A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 607 through 610 No H-bonds generated for 'chain 'A' and resid 607 through 610' Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.551A pdb=" N SER A 689 " --> pdb=" O MET A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 711 Processing helix chain 'A' and resid 754 through 757 No H-bonds generated for 'chain 'A' and resid 754 through 757' Processing helix chain 'A' and resid 767 through 772 Processing helix chain 'A' and resid 779 through 783 Processing helix chain 'A' and resid 794 through 806 removed outlier: 4.453A pdb=" N GLU A 798 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE A 799 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 838 through 851 Processing helix chain 'A' and resid 971 through 1011 removed outlier: 3.901A pdb=" N ARG A 982 " --> pdb=" O ARG A 979 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A1008 " --> pdb=" O SER A1005 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A1009 " --> pdb=" O LEU A1006 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR A1010 " --> pdb=" O SER A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1036 removed outlier: 3.889A pdb=" N LEU A1027 " --> pdb=" O VAL A1023 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1083 Processing helix chain 'A' and resid 1100 through 1118 removed outlier: 4.074A pdb=" N ILE A1108 " --> pdb=" O GLY A1104 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A1117 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1151 Processing helix chain 'A' and resid 1156 through 1161 Processing helix chain 'A' and resid 1169 through 1196 Processing helix chain 'B' and resid 2 through 19 Processing sheet with id= A, first strand: chain 'A' and resid 111 through 114 Processing sheet with id= B, first strand: chain 'A' and resid 256 through 260 Processing sheet with id= C, first strand: chain 'A' and resid 277 through 280 removed outlier: 7.092A pdb=" N ASP A 292 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 467 through 469 Processing sheet with id= E, first strand: chain 'A' and resid 664 through 667 removed outlier: 7.252A pdb=" N LEU A 638 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 600 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER A 594 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE A 576 " --> pdb=" O SER A 594 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 742 through 744 removed outlier: 3.732A pdb=" N ASP A 722 " --> pdb=" O LEU A 733 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP A 762 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LEU A 721 " --> pdb=" O ASP A 762 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA A 764 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N ARG A 723 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TRP A 787 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL A 765 " --> pdb=" O TRP A 787 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR A 789 " --> pdb=" O VAL A 765 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 299 through 303 removed outlier: 3.829A pdb=" N GLN A 347 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASN A 303 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA A 345 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 498 through 501 removed outlier: 6.852A pdb=" N ILE A 670 " --> pdb=" O GLU A 500 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 930 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: 2.79 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2701 1.34 - 1.46: 1481 1.46 - 1.57: 4335 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 8580 Sorted by residual: bond pdb=" BE BEF A1301 " pdb=" F2 BEF A1301 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" BE BEF A1301 " pdb=" F3 BEF A1301 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" BE BEF A1301 " pdb=" F1 BEF A1301 " ideal model delta sigma weight residual 1.476 1.534 -0.058 2.00e-02 2.50e+03 8.54e+00 bond pdb=" N VAL A 29 " pdb=" CA VAL A 29 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.19e-02 7.06e+03 4.64e+00 bond pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 1.524 1.547 -0.023 1.23e-02 6.61e+03 3.56e+00 ... (remaining 8575 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.91: 203 105.91 - 112.95: 4735 112.95 - 119.99: 2808 119.99 - 127.03: 3814 127.03 - 134.07: 87 Bond angle restraints: 11647 Sorted by residual: angle pdb=" N VAL A 29 " pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 110.53 117.10 -6.57 9.40e-01 1.13e+00 4.88e+01 angle pdb=" C LEU A 30 " pdb=" N PRO A 31 " pdb=" CA PRO A 31 " ideal model delta sigma weight residual 118.85 126.10 -7.25 1.09e+00 8.42e-01 4.43e+01 angle pdb=" N PRO A 34 " pdb=" CA PRO A 34 " pdb=" CB PRO A 34 " ideal model delta sigma weight residual 103.33 109.78 -6.45 1.10e+00 8.26e-01 3.44e+01 angle pdb=" C LYS A 26 " pdb=" N PRO A 27 " pdb=" CA PRO A 27 " ideal model delta sigma weight residual 119.05 125.22 -6.17 1.11e+00 8.12e-01 3.09e+01 angle pdb=" F2 BEF A1301 " pdb=" BE BEF A1301 " pdb=" F3 BEF A1301 " ideal model delta sigma weight residual 119.96 107.22 12.74 3.00e+00 1.11e-01 1.80e+01 ... (remaining 11642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4791 17.94 - 35.88: 302 35.88 - 53.81: 38 53.81 - 71.75: 6 71.75 - 89.69: 4 Dihedral angle restraints: 5141 sinusoidal: 1922 harmonic: 3219 Sorted by residual: dihedral pdb=" CA TYR A 761 " pdb=" C TYR A 761 " pdb=" N ASP A 762 " pdb=" CA ASP A 762 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TYR A1121 " pdb=" C TYR A1121 " pdb=" N GLN A1122 " pdb=" CA GLN A1122 " ideal model delta harmonic sigma weight residual -180.00 -161.29 -18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" N PRO A 34 " pdb=" C PRO A 34 " pdb=" CA PRO A 34 " pdb=" CB PRO A 34 " ideal model delta harmonic sigma weight residual 115.10 123.27 -8.17 0 2.50e+00 1.60e-01 1.07e+01 ... (remaining 5138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1140 0.052 - 0.105: 194 0.105 - 0.157: 32 0.157 - 0.210: 2 0.210 - 0.262: 3 Chirality restraints: 1371 Sorted by residual: chirality pdb=" CA PRO A 34 " pdb=" N PRO A 34 " pdb=" C PRO A 34 " pdb=" CB PRO A 34 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CG LEU A 73 " pdb=" CB LEU A 73 " pdb=" CD1 LEU A 73 " pdb=" CD2 LEU A 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CG LEU A 30 " pdb=" CB LEU A 30 " pdb=" CD1 LEU A 30 " pdb=" CD2 LEU A 30 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1368 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 29 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C VAL A 29 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A 29 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 30 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 30 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A 31 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1006 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.81e+00 pdb=" C LEU A1006 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU A1006 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A1007 " 0.010 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 41 2.54 - 3.13: 6578 3.13 - 3.72: 12161 3.72 - 4.31: 16144 4.31 - 4.90: 28136 Nonbonded interactions: 63060 Sorted by model distance: nonbonded pdb=" F1 BEF A1301 " pdb="MG MG A1302 " model vdw 1.956 2.120 nonbonded pdb=" OD2 ASP A 487 " pdb=" F1 BEF A1301 " model vdw 1.959 2.390 nonbonded pdb=" OD2 ASP A 487 " pdb="MG MG A1302 " model vdw 2.194 2.170 nonbonded pdb=" OG SER A 506 " pdb=" OH TYR A 516 " model vdw 2.237 2.440 nonbonded pdb=" OG SER A1099 " pdb=" OD1 ASN A1102 " model vdw 2.241 2.440 ... (remaining 63055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.000 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.330 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 0.084 8580 Z= 0.248 Angle : 0.585 12.740 11647 Z= 0.329 Chirality : 0.042 0.262 1371 Planarity : 0.004 0.042 1478 Dihedral : 11.801 89.690 3053 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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: -2.43 (0.22), residues: 1080 helix: 0.00 (0.22), residues: 478 sheet: -2.86 (0.40), residues: 120 loop : -3.02 (0.21), residues: 482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.915 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2071 time to fit residues: 16.4265 Evaluate side-chains 37 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 0.0040 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 107 ASN A 196 HIS ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 HIS A 990 GLN A1050 GLN A1122 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8580 Z= 0.146 Angle : 0.495 7.747 11647 Z= 0.252 Chirality : 0.039 0.173 1371 Planarity : 0.004 0.032 1478 Dihedral : 3.770 19.866 1167 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.57 % Allowed : 8.42 % Favored : 91.01 % 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: -1.59 (0.24), residues: 1080 helix: 0.73 (0.24), residues: 483 sheet: -2.79 (0.36), residues: 142 loop : -2.49 (0.23), residues: 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.981 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 40 average time/residue: 0.1607 time to fit residues: 10.7185 Evaluate side-chains 38 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.999 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0817 time to fit residues: 1.4992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 109 optimal weight: 50.0000 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8580 Z= 0.343 Angle : 0.575 13.165 11647 Z= 0.288 Chirality : 0.042 0.159 1371 Planarity : 0.004 0.039 1478 Dihedral : 4.080 20.361 1167 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.80 % Allowed : 12.06 % Favored : 87.14 % 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: -1.26 (0.25), residues: 1080 helix: 1.02 (0.25), residues: 476 sheet: -2.72 (0.36), residues: 148 loop : -2.23 (0.24), residues: 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 1.039 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 43 average time/residue: 0.1552 time to fit residues: 11.1665 Evaluate side-chains 39 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0872 time to fit residues: 1.6234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8580 Z= 0.204 Angle : 0.490 11.159 11647 Z= 0.247 Chirality : 0.040 0.182 1371 Planarity : 0.004 0.035 1478 Dihedral : 3.878 20.341 1167 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.25 % Allowed : 13.65 % Favored : 85.10 % 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: -0.93 (0.25), residues: 1080 helix: 1.24 (0.25), residues: 476 sheet: -2.44 (0.36), residues: 149 loop : -2.02 (0.24), residues: 455 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.968 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 48 average time/residue: 0.1574 time to fit residues: 12.5913 Evaluate side-chains 41 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0916 time to fit residues: 1.9918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8580 Z= 0.225 Angle : 0.500 10.340 11647 Z= 0.251 Chirality : 0.040 0.188 1371 Planarity : 0.004 0.036 1478 Dihedral : 3.852 20.303 1167 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.91 % Allowed : 15.70 % Favored : 83.39 % 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: -0.71 (0.25), residues: 1080 helix: 1.38 (0.25), residues: 475 sheet: -2.16 (0.38), residues: 145 loop : -1.91 (0.25), residues: 460 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 1.062 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 46 average time/residue: 0.1795 time to fit residues: 13.5019 Evaluate side-chains 40 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0861 time to fit residues: 1.6773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 0.0970 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8580 Z= 0.180 Angle : 0.487 9.741 11647 Z= 0.243 Chirality : 0.040 0.198 1371 Planarity : 0.004 0.034 1478 Dihedral : 3.764 20.202 1167 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.91 % Allowed : 16.38 % Favored : 82.71 % 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: -0.52 (0.25), residues: 1080 helix: 1.49 (0.25), residues: 473 sheet: -1.87 (0.39), residues: 140 loop : -1.82 (0.25), residues: 467 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 1.020 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 47 average time/residue: 0.1557 time to fit residues: 12.2514 Evaluate side-chains 40 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0777 time to fit residues: 1.6331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.0570 chunk 42 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8580 Z= 0.127 Angle : 0.514 14.325 11647 Z= 0.247 Chirality : 0.040 0.221 1371 Planarity : 0.003 0.032 1478 Dihedral : 3.613 19.744 1167 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.91 % Allowed : 16.50 % Favored : 82.59 % 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: -0.32 (0.25), residues: 1080 helix: 1.55 (0.25), residues: 473 sheet: -1.62 (0.41), residues: 140 loop : -1.65 (0.25), residues: 467 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.961 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 43 average time/residue: 0.1537 time to fit residues: 11.1994 Evaluate side-chains 39 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0768 time to fit residues: 1.5572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 97 optimal weight: 0.0270 chunk 102 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8580 Z= 0.314 Angle : 0.569 12.773 11647 Z= 0.284 Chirality : 0.041 0.197 1371 Planarity : 0.004 0.035 1478 Dihedral : 3.918 20.300 1167 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.91 % Allowed : 17.06 % Favored : 82.03 % 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: -0.29 (0.25), residues: 1080 helix: 1.63 (0.25), residues: 473 sheet: -1.68 (0.41), residues: 140 loop : -1.68 (0.25), residues: 467 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.915 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 43 average time/residue: 0.1536 time to fit residues: 11.1763 Evaluate side-chains 41 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 1.032 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0825 time to fit residues: 1.9914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1050 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8580 Z= 0.201 Angle : 0.536 12.153 11647 Z= 0.262 Chirality : 0.040 0.209 1371 Planarity : 0.004 0.033 1478 Dihedral : 3.795 20.499 1167 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.23 % Allowed : 17.52 % Favored : 82.25 % 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: -0.14 (0.25), residues: 1080 helix: 1.75 (0.25), residues: 469 sheet: -1.51 (0.41), residues: 140 loop : -1.59 (0.25), residues: 471 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.985 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 39 average time/residue: 0.1618 time to fit residues: 10.5964 Evaluate side-chains 36 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 30.0000 chunk 101 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 8580 Z= 0.367 Angle : 0.588 12.899 11647 Z= 0.295 Chirality : 0.042 0.205 1371 Planarity : 0.004 0.035 1478 Dihedral : 4.038 20.441 1167 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 18.32 % Favored : 81.68 % 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 (0.26), residues: 1080 helix: 1.74 (0.25), residues: 467 sheet: -1.63 (0.41), residues: 140 loop : -1.69 (0.25), residues: 473 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.947 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1640 time to fit residues: 10.4004 Evaluate side-chains 37 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.075429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.054674 restraints weight = 28380.387| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.32 r_work: 0.2933 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8580 Z= 0.163 Angle : 0.532 12.074 11647 Z= 0.262 Chirality : 0.040 0.204 1371 Planarity : 0.004 0.034 1478 Dihedral : 3.829 20.548 1167 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 18.66 % Favored : 81.34 % 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: -0.13 (0.25), residues: 1080 helix: 1.79 (0.25), residues: 468 sheet: -1.51 (0.40), residues: 151 loop : -1.60 (0.26), residues: 461 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1574.13 seconds wall clock time: 29 minutes 26.61 seconds (1766.61 seconds total)