Starting phenix.real_space_refine on Wed Sep 17 08:18:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qa6_52972/09_2025/9qa6_52972_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qa6_52972/09_2025/9qa6_52972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qa6_52972/09_2025/9qa6_52972_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qa6_52972/09_2025/9qa6_52972_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qa6_52972/09_2025/9qa6_52972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qa6_52972/09_2025/9qa6_52972.map" } resolution = 2.81 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 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= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 27 5.16 5 C 4349 2.51 5 N 1161 2.21 5 O 1503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7043 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6862 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 845, 6750 Classifications: {'peptide': 845} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 810} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1, 'CME:plan-1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 845, 6750 Classifications: {'peptide': 845} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 810} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1, 'CME:plan-1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 6802 Conformer: "C" Number of residues, atoms: 845, 6654 Classifications: {'peptide': 845} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 810} Unresolved chain link angles: 30 Unresolved chain link dihedrals: 60 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 1, 'CME:plan-1': 1, 'TYR:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 bond proxies already assigned to first conformer: 6802 Chain: "A" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 181 Unusual residues: {' ZN': 3, 'AZI': 7, 'GOL': 1} Classifications: {'undetermined': 11, 'water': 151} Link IDs: {None: 161} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 752 SG CYS A 126 31.263 34.129 29.722 1.00 97.57 S ATOM 4669 SG CYS A 606 29.375 47.870 68.702 1.00 86.15 S ATOM 4757 SG CYS A 616 28.388 49.300 72.157 1.00 92.76 S ATOM 4779 SG CYS A 619 27.957 45.879 71.500 1.00 79.84 S Time building chain proxies: 4.28, per 1000 atoms: 0.61 Number of scatterers: 7043 At special positions: 0 Unit cell: (73.73, 85.41, 110.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 27 16.00 O 1503 8.00 N 1161 7.00 C 4349 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 780.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 90 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 126 " pdb=" ZN A1202 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 606 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 619 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 616 " pdb=" ZN A1203 " pdb="ZN ZN A1203 " - pdb=" NE2 HIS A 543 " pdb="ZN ZN A1203 " - pdb=" NE2 HIS A 539 " 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 22.8% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.802A pdb=" N ARG A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 93' Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 107 through 114 Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 191 through 196 removed outlier: 4.406A pdb=" N VAL A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 380 through 398 removed outlier: 3.894A pdb=" N PHE A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A 398 " --> pdb=" O ASP A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 5.171A pdb=" N ASP A 406 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 458 through 467 removed outlier: 3.782A pdb=" N GLU A 462 " --> pdb=" O CYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 491 through 497 removed outlier: 4.182A pdb=" N ASP A 495 " --> pdb=" O TYR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 520 Processing helix chain 'A' and resid 532 through 545 Processing helix chain 'A' and resid 558 through 565 Processing helix chain 'A' and resid 616 through 631 Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'A' and resid 660 through 675 Processing helix chain 'A' and resid 677 through 684 removed outlier: 4.395A pdb=" N SER A 682 " --> pdb=" O ASN A 679 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A 684 " --> pdb=" O LYS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 749 removed outlier: 4.049A pdb=" N ALA A 747 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 47 removed outlier: 4.035A pdb=" N ILE A 52 " --> pdb=" O MET A 44 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL A 46 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N CYS A 56 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 67 " --> pdb=" O CYS A 56 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 58 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 74 removed outlier: 4.006A pdb=" N ASP A 73 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 167 Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233 removed outlier: 4.244A pdb=" N ALA A 232 " --> pdb=" O TRP A 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 242 through 247 removed outlier: 4.504A pdb=" N ARG A 256 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 288 through 291 removed outlier: 5.274A pdb=" N THR A 289 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N SER A 303 " --> pdb=" O THR A 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 332 through 334 removed outlier: 6.221A pdb=" N VAL A 410 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N MET A 367 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N TYR A 411 " --> pdb=" O MET A 367 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL A 369 " --> pdb=" O TYR A 411 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU A 413 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL A 371 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 499 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE A 500 " --> pdb=" O PHE A 524 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N SER A 526 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N MET A 502 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 431 through 433 Processing sheet with id=AA9, first strand: chain 'A' and resid 568 through 569 Processing sheet with id=AB1, first strand: chain 'A' and resid 636 through 638 Processing sheet with id=AB2, first strand: chain 'A' and resid 636 through 638 Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 740 removed outlier: 3.531A pdb=" N ALA A 800 " --> pdb=" O VAL A 791 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 831 through 835 removed outlier: 6.381A pdb=" N LYS A 875 " --> pdb=" O PHE A 853 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE A 853 " --> pdb=" O LYS A 875 " (cutoff:3.500A) 195 hydrogen bonds defined for protein. 501 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: 1.23 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.34: 2210 1.34 - 1.52: 2892 1.52 - 1.69: 1930 1.69 - 1.87: 41 1.87 - 2.05: 1 Bond restraints: 7074 Sorted by residual: bond pdb=" CB ARG A 165 " pdb=" CG ARG A 165 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.66e+00 bond pdb=" CB GLU A 823 " pdb=" CG GLU A 823 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.55e+00 bond pdb=" CB HIS A 543 " pdb=" CG HIS A 543 " ideal model delta sigma weight residual 1.497 1.477 0.020 1.40e-02 5.10e+03 2.12e+00 bond pdb=" CB THR A 74 " pdb=" CG2 THR A 74 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.08e+00 bond pdb=" SD MET A 255 " pdb=" CE MET A 255 " ideal model delta sigma weight residual 1.791 1.757 0.034 2.50e-02 1.60e+03 1.86e+00 ... (remaining 7069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 9085 1.75 - 3.50: 453 3.50 - 5.24: 62 5.24 - 6.99: 7 6.99 - 8.74: 6 Bond angle restraints: 9613 Sorted by residual: angle pdb=" CA TYR A 242 " pdb=" CB TYR A 242 " pdb=" CG TYR A 242 " ideal model delta sigma weight residual 113.90 122.64 -8.74 1.80e+00 3.09e-01 2.36e+01 angle pdb=" CA BTYR A 286 " pdb=" CB BTYR A 286 " pdb=" CG BTYR A 286 " ideal model delta sigma weight residual 113.90 105.99 7.91 1.80e+00 3.09e-01 1.93e+01 angle pdb=" CA TYR A 141 " pdb=" CB TYR A 141 " pdb=" CG TYR A 141 " ideal model delta sigma weight residual 113.90 121.81 -7.91 1.80e+00 3.09e-01 1.93e+01 angle pdb=" C GLU A 285 " pdb=" N TYR A 286 " pdb=" CA BTYR A 286 " ideal model delta sigma weight residual 122.06 114.25 7.81 1.86e+00 2.89e-01 1.76e+01 angle pdb=" CA TYR A 173 " pdb=" CB TYR A 173 " pdb=" CG TYR A 173 " ideal model delta sigma weight residual 113.90 121.36 -7.46 1.80e+00 3.09e-01 1.72e+01 ... (remaining 9608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 3688 15.43 - 30.85: 374 30.85 - 46.28: 88 46.28 - 61.70: 51 61.70 - 77.12: 9 Dihedral angle restraints: 4210 sinusoidal: 1656 harmonic: 2554 Sorted by residual: dihedral pdb=" CA TYR A 141 " pdb=" C TYR A 141 " pdb=" N ASN A 142 " pdb=" CA ASN A 142 " ideal model delta harmonic sigma weight residual 180.00 153.47 26.53 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA GLU A 399 " pdb=" C GLU A 399 " pdb=" N PRO A 400 " pdb=" CA PRO A 400 " ideal model delta harmonic sigma weight residual 0.00 20.92 -20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ASP A 181 " pdb=" C ASP A 181 " pdb=" N ALA A 182 " pdb=" CA ALA A 182 " ideal model delta harmonic sigma weight residual -180.00 -159.16 -20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 4207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 623 0.040 - 0.080: 274 0.080 - 0.120: 85 0.120 - 0.160: 14 0.160 - 0.200: 7 Chirality restraints: 1003 Sorted by residual: chirality pdb=" CA TYR A 141 " pdb=" N TYR A 141 " pdb=" C TYR A 141 " pdb=" CB TYR A 141 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA BTYR A 286 " pdb=" N TYR A 286 " pdb=" C TYR A 286 " pdb=" CB BTYR A 286 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA HIS A 170 " pdb=" N HIS A 170 " pdb=" C HIS A 170 " pdb=" CB HIS A 170 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 1000 not shown) Planarity restraints: 1252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 529 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ASP A 529 " -0.055 2.00e-02 2.50e+03 pdb=" O ASP A 529 " 0.021 2.00e-02 2.50e+03 pdb=" N SER A 530 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 286 " -0.033 2.00e-02 2.50e+03 1.93e-02 7.44e+00 pdb=" CG BTYR A 286 " 0.038 2.00e-02 2.50e+03 pdb=" CD1BTYR A 286 " 0.015 2.00e-02 2.50e+03 pdb=" CD2BTYR A 286 " 0.003 2.00e-02 2.50e+03 pdb=" CE1BTYR A 286 " -0.013 2.00e-02 2.50e+03 pdb=" CE2BTYR A 286 " 0.000 2.00e-02 2.50e+03 pdb=" CZ BTYR A 286 " -0.004 2.00e-02 2.50e+03 pdb=" OH BTYR A 286 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 242 " 0.026 2.00e-02 2.50e+03 1.73e-02 6.02e+00 pdb=" CG TYR A 242 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 242 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 242 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 242 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 242 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 242 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 242 " 0.003 2.00e-02 2.50e+03 ... (remaining 1249 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 21 2.60 - 3.17: 6120 3.17 - 3.75: 11416 3.75 - 4.32: 17409 4.32 - 4.90: 28088 Nonbonded interactions: 63054 Sorted by model distance: nonbonded pdb=" OD1 ASP A 550 " pdb="ZN ZN A1203 " model vdw 2.022 2.230 nonbonded pdb=" OD2 ASP A 78 " pdb="ZN ZN A1201 " model vdw 2.083 2.230 nonbonded pdb="ZN ZN A1203 " pdb=" O3 GOL A1204 " model vdw 2.096 2.230 nonbonded pdb=" OD1 ASP A 78 " pdb="ZN ZN A1201 " model vdw 2.124 2.230 nonbonded pdb=" OE2 GLU A 551 " pdb="ZN ZN A1202 " model vdw 2.173 2.230 ... (remaining 63049 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=0.19 max=1.00 mean=0.98 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: 3.200 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.320 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:8.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 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 : 0.008 0.334 7081 Z= 0.335 Angle : 0.875 8.738 9613 Z= 0.515 Chirality : 0.050 0.200 1003 Planarity : 0.008 0.090 1252 Dihedral : 15.059 77.124 2598 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 5.01 % Allowed : 10.03 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.27), residues: 856 helix: -0.60 (0.41), residues: 141 sheet: 0.41 (0.39), residues: 163 loop : 0.04 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 532 TYR 0.041 0.003 TYR A 242 PHE 0.036 0.004 PHE A 524 TRP 0.017 0.003 TRP A 54 HIS 0.008 0.003 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00598 ( 7074) covalent geometry : angle 0.87531 ( 9613) hydrogen bonds : bond 0.14982 ( 193) hydrogen bonds : angle 8.08867 ( 501) metal coordination : bond 0.18104 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 36 ILE cc_start: 0.6943 (mm) cc_final: 0.6738 (mm) REVERT: A 48 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7705 (t0) REVERT: A 142 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8201 (p0) REVERT: A 143 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8211 (mm-30) REVERT: A 658 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7022 (t0) REVERT: A 745 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7328 (t70) REVERT: A 846 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8449 (ttmm) outliers start: 28 outliers final: 6 residues processed: 95 average time/residue: 0.5112 time to fit residues: 51.7438 Evaluate side-chains 60 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 745 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 393 GLN B A 423 ASN A A 437 ASN A 687 ASN A A 706 ASN A A 706 ASN B A 733 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.097545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.070790 restraints weight = 63260.923| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 4.96 r_work: 0.2751 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7081 Z= 0.163 Angle : 0.571 6.424 9613 Z= 0.315 Chirality : 0.044 0.170 1003 Planarity : 0.004 0.046 1252 Dihedral : 6.364 40.662 998 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.24 % Allowed : 13.98 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.27), residues: 856 helix: 0.35 (0.45), residues: 136 sheet: 0.55 (0.40), residues: 154 loop : 0.06 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 683 TYR 0.022 0.002 TYR A 173 PHE 0.019 0.002 PHE A 524 TRP 0.013 0.001 TRP A 223 HIS 0.008 0.002 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 7074) covalent geometry : angle 0.57061 ( 9613) hydrogen bonds : bond 0.03912 ( 193) hydrogen bonds : angle 6.14244 ( 501) metal coordination : bond 0.00550 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.267 Fit side-chains REVERT: A 48 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7548 (t0) REVERT: A 322 ASN cc_start: 0.8092 (p0) cc_final: 0.7864 (p0) REVERT: A 658 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7247 (t0) REVERT: A 725 THR cc_start: 0.9099 (p) cc_final: 0.8800 (t) REVERT: A 745 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.7857 (t70) outliers start: 8 outliers final: 2 residues processed: 65 average time/residue: 0.4929 time to fit residues: 34.3382 Evaluate side-chains 46 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 745 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.096791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.071313 restraints weight = 58629.061| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 4.69 r_work: 0.2755 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7081 Z= 0.140 Angle : 0.553 8.206 9613 Z= 0.300 Chirality : 0.043 0.193 1003 Planarity : 0.004 0.054 1252 Dihedral : 5.480 39.428 986 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.24 % Allowed : 15.17 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.28), residues: 856 helix: 0.52 (0.46), residues: 135 sheet: 0.52 (0.40), residues: 153 loop : 0.10 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 683 TYR 0.023 0.001 TYR A 173 PHE 0.015 0.001 PHE A 524 TRP 0.012 0.001 TRP A 579 HIS 0.007 0.002 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 7074) covalent geometry : angle 0.55284 ( 9613) hydrogen bonds : bond 0.03572 ( 193) hydrogen bonds : angle 5.87960 ( 501) metal coordination : bond 0.00374 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.275 Fit side-chains REVERT: A 48 ASN cc_start: 0.8069 (OUTLIER) cc_final: 0.7558 (t0) REVERT: A 658 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7272 (t0) REVERT: A 725 THR cc_start: 0.9066 (p) cc_final: 0.8837 (t) REVERT: A 745 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.7958 (t70) outliers start: 8 outliers final: 2 residues processed: 51 average time/residue: 0.5023 time to fit residues: 27.5761 Evaluate side-chains 47 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 745 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 31 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.095102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.069810 restraints weight = 56271.175| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 4.57 r_work: 0.2733 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7081 Z= 0.166 Angle : 0.552 9.715 9613 Z= 0.299 Chirality : 0.044 0.244 1003 Planarity : 0.004 0.051 1252 Dihedral : 5.284 37.609 986 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.51 % Allowed : 15.57 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.28), residues: 856 helix: 0.52 (0.46), residues: 135 sheet: 0.18 (0.38), residues: 170 loop : 0.14 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 683 TYR 0.024 0.002 TYR A 173 PHE 0.013 0.001 PHE A 524 TRP 0.010 0.001 TRP A 223 HIS 0.007 0.002 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 7074) covalent geometry : angle 0.55185 ( 9613) hydrogen bonds : bond 0.03645 ( 193) hydrogen bonds : angle 5.84098 ( 501) metal coordination : bond 0.00407 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.344 Fit side-chains REVERT: A 48 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7620 (t0) REVERT: A 313 THR cc_start: 0.8728 (p) cc_final: 0.8499 (p) REVERT: A 322 ASN cc_start: 0.7934 (p0) cc_final: 0.7693 (p0) REVERT: A 658 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7329 (t0) REVERT: A 745 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8063 (t70) outliers start: 9 outliers final: 1 residues processed: 51 average time/residue: 0.4522 time to fit residues: 25.0685 Evaluate side-chains 42 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 745 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.1980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.095626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.070259 restraints weight = 58770.656| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.65 r_work: 0.2742 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7081 Z= 0.137 Angle : 0.519 8.977 9613 Z= 0.279 Chirality : 0.043 0.241 1003 Planarity : 0.004 0.052 1252 Dihedral : 5.009 37.154 984 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.85 % Allowed : 15.57 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.28), residues: 856 helix: 0.63 (0.47), residues: 135 sheet: 0.22 (0.38), residues: 174 loop : 0.15 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 683 TYR 0.023 0.002 TYR A 173 PHE 0.013 0.001 PHE A 524 TRP 0.010 0.001 TRP A 223 HIS 0.007 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7074) covalent geometry : angle 0.51944 ( 9613) hydrogen bonds : bond 0.03287 ( 193) hydrogen bonds : angle 5.71310 ( 501) metal coordination : bond 0.00335 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.383 Fit side-chains REVERT: A 48 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7622 (t0) REVERT: A 313 THR cc_start: 0.8733 (p) cc_final: 0.8508 (p) REVERT: A 322 ASN cc_start: 0.8011 (p0) cc_final: 0.7772 (p0) REVERT: A 658 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7321 (t0) outliers start: 4 outliers final: 1 residues processed: 46 average time/residue: 0.4932 time to fit residues: 24.5178 Evaluate side-chains 42 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 658 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.096861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.071459 restraints weight = 62081.875| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 4.76 r_work: 0.2757 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7081 Z= 0.117 Angle : 0.504 9.385 9613 Z= 0.269 Chirality : 0.042 0.234 1003 Planarity : 0.004 0.049 1252 Dihedral : 4.713 37.394 982 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.85 % Allowed : 15.57 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.29), residues: 856 helix: 0.69 (0.47), residues: 135 sheet: 0.40 (0.39), residues: 165 loop : 0.07 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 683 TYR 0.022 0.001 TYR A 173 PHE 0.012 0.001 PHE A 524 TRP 0.011 0.001 TRP A 223 HIS 0.007 0.002 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7074) covalent geometry : angle 0.50443 ( 9613) hydrogen bonds : bond 0.03114 ( 193) hydrogen bonds : angle 5.60146 ( 501) metal coordination : bond 0.00268 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.227 Fit side-chains REVERT: A 48 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7598 (t0) REVERT: A 296 GLN cc_start: 0.8631 (tt0) cc_final: 0.8396 (tm-30) REVERT: A 313 THR cc_start: 0.8698 (p) cc_final: 0.8471 (p) REVERT: A 322 ASN cc_start: 0.8078 (p0) cc_final: 0.7833 (p0) REVERT: A 658 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7268 (t0) REVERT: A 745 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8042 (t70) outliers start: 5 outliers final: 1 residues processed: 46 average time/residue: 0.4844 time to fit residues: 23.9888 Evaluate side-chains 45 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 745 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.093964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.068747 restraints weight = 54463.723| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 4.53 r_work: 0.2714 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7081 Z= 0.186 Angle : 0.537 6.374 9613 Z= 0.290 Chirality : 0.044 0.243 1003 Planarity : 0.004 0.049 1252 Dihedral : 4.907 34.170 982 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.85 % Allowed : 15.44 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.29), residues: 856 helix: 0.58 (0.46), residues: 135 sheet: 0.20 (0.38), residues: 176 loop : 0.11 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 683 TYR 0.025 0.002 TYR A 487 PHE 0.012 0.001 PHE A 510 TRP 0.011 0.001 TRP A 392 HIS 0.006 0.002 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 7074) covalent geometry : angle 0.53740 ( 9613) hydrogen bonds : bond 0.03595 ( 193) hydrogen bonds : angle 5.74134 ( 501) metal coordination : bond 0.00461 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.291 Fit side-chains REVERT: A 48 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7672 (t0) REVERT: A 296 GLN cc_start: 0.8652 (tt0) cc_final: 0.8389 (tm-30) REVERT: A 313 THR cc_start: 0.8826 (p) cc_final: 0.8608 (p) REVERT: A 322 ASN cc_start: 0.8147 (p0) cc_final: 0.7917 (p0) REVERT: A 745 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8089 (t70) outliers start: 5 outliers final: 1 residues processed: 46 average time/residue: 0.4917 time to fit residues: 24.4814 Evaluate side-chains 42 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 745 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.093029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.067303 restraints weight = 70827.683| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 4.95 r_work: 0.2680 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7081 Z= 0.214 Angle : 0.562 9.667 9613 Z= 0.302 Chirality : 0.045 0.238 1003 Planarity : 0.004 0.049 1252 Dihedral : 4.913 34.102 980 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.72 % Allowed : 15.70 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.29), residues: 856 helix: 0.42 (0.46), residues: 135 sheet: -0.02 (0.38), residues: 175 loop : 0.06 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 683 TYR 0.025 0.002 TYR A 173 PHE 0.014 0.002 PHE A 287 TRP 0.011 0.001 TRP A 392 HIS 0.006 0.002 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 7074) covalent geometry : angle 0.56156 ( 9613) hydrogen bonds : bond 0.03749 ( 193) hydrogen bonds : angle 5.80161 ( 501) metal coordination : bond 0.00520 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.289 Fit side-chains REVERT: A 48 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7788 (t0) REVERT: A 296 GLN cc_start: 0.8651 (tt0) cc_final: 0.8395 (tm-30) REVERT: A 313 THR cc_start: 0.8923 (p) cc_final: 0.8707 (p) REVERT: A 322 ASN cc_start: 0.8164 (p0) cc_final: 0.7951 (p0) REVERT: A 658 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7527 (t0) REVERT: A 745 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8148 (t70) outliers start: 4 outliers final: 1 residues processed: 42 average time/residue: 0.4995 time to fit residues: 22.7140 Evaluate side-chains 42 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 745 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 77 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.095173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.070319 restraints weight = 47076.975| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 4.30 r_work: 0.2748 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7081 Z= 0.138 Angle : 0.517 6.693 9613 Z= 0.277 Chirality : 0.043 0.235 1003 Planarity : 0.004 0.049 1252 Dihedral : 4.696 34.536 980 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.58 % Allowed : 16.23 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.29), residues: 856 helix: 0.59 (0.46), residues: 135 sheet: 0.08 (0.38), residues: 173 loop : 0.06 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 683 TYR 0.023 0.001 TYR A 173 PHE 0.012 0.001 PHE A 524 TRP 0.010 0.001 TRP A 223 HIS 0.006 0.002 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7074) covalent geometry : angle 0.51718 ( 9613) hydrogen bonds : bond 0.03226 ( 193) hydrogen bonds : angle 5.62420 ( 501) metal coordination : bond 0.00317 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.274 Fit side-chains REVERT: A 48 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7729 (t0) REVERT: A 296 GLN cc_start: 0.8618 (tt0) cc_final: 0.8342 (tm-30) REVERT: A 313 THR cc_start: 0.8890 (p) cc_final: 0.8675 (p) REVERT: A 322 ASN cc_start: 0.8120 (p0) cc_final: 0.7893 (p0) REVERT: A 658 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7372 (t0) outliers start: 3 outliers final: 1 residues processed: 42 average time/residue: 0.4811 time to fit residues: 21.9336 Evaluate side-chains 41 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 658 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.069002 restraints weight = 62520.056| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 4.78 r_work: 0.2716 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7081 Z= 0.159 Angle : 0.531 10.126 9613 Z= 0.284 Chirality : 0.043 0.238 1003 Planarity : 0.004 0.048 1252 Dihedral : 4.699 34.430 980 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.72 % Allowed : 16.23 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.29), residues: 856 helix: 0.56 (0.46), residues: 135 sheet: -0.13 (0.38), residues: 180 loop : 0.14 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 683 TYR 0.024 0.002 TYR A 173 PHE 0.011 0.001 PHE A 287 TRP 0.010 0.001 TRP A 223 HIS 0.006 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 7074) covalent geometry : angle 0.53148 ( 9613) hydrogen bonds : bond 0.03356 ( 193) hydrogen bonds : angle 5.65506 ( 501) metal coordination : bond 0.00383 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.273 Fit side-chains REVERT: A 48 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7754 (t0) REVERT: A 296 GLN cc_start: 0.8615 (tt0) cc_final: 0.8345 (tm-30) REVERT: A 313 THR cc_start: 0.8906 (p) cc_final: 0.8693 (p) REVERT: A 322 ASN cc_start: 0.8181 (p0) cc_final: 0.7958 (p0) REVERT: A 658 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7411 (t0) REVERT: A 745 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8132 (t70) outliers start: 4 outliers final: 1 residues processed: 44 average time/residue: 0.4866 time to fit residues: 23.0692 Evaluate side-chains 43 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 745 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 0.0050 chunk 60 optimal weight: 0.0370 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 0.5472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.095961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.070698 restraints weight = 56383.901| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 4.63 r_work: 0.2753 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7081 Z= 0.115 Angle : 0.502 6.918 9613 Z= 0.270 Chirality : 0.042 0.229 1003 Planarity : 0.004 0.049 1252 Dihedral : 4.580 34.721 980 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.72 % Allowed : 16.09 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.29), residues: 856 helix: 0.72 (0.47), residues: 135 sheet: 0.09 (0.38), residues: 173 loop : 0.06 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 683 TYR 0.023 0.001 TYR A 173 PHE 0.012 0.001 PHE A 524 TRP 0.011 0.001 TRP A 223 HIS 0.006 0.001 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7074) covalent geometry : angle 0.50219 ( 9613) hydrogen bonds : bond 0.03050 ( 193) hydrogen bonds : angle 5.55807 ( 501) metal coordination : bond 0.00238 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2457.23 seconds wall clock time: 42 minutes 45.74 seconds (2565.74 seconds total)