Starting phenix.real_space_refine on Fri Jul 25 04:22:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qa6_52972/07_2025/9qa6_52972_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qa6_52972/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9qa6_52972/07_2025/9qa6_52972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qa6_52972/07_2025/9qa6_52972.map" model { file = "/net/cci-nas-00/data/ceres_data/9qa6_52972/07_2025/9qa6_52972_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qa6_52972/07_2025/9qa6_52972_neut.cif" } resolution = 2.81 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= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'CME:plan-1': 1, 'ASP:plan': 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: {'CME:plan-1': 1, 'ASP:plan': 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: {'GLN:plan1': 2, 'CME:plan-1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'TYR:plan': 2, '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: 11.35, per 1000 atoms: 1.61 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: 2.24 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 0.98 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: 2.74 Time building geometry restraints manager: 2.50 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: 2.690 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 33.110 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.070 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:14.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.720 ------------------------------------------------------------------------------- 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 (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: -0.08 (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 TRP 0.017 0.003 TRP A 54 HIS 0.008 0.003 HIS A 170 PHE 0.036 0.004 PHE A 524 TYR 0.041 0.003 TYR A 242 ARG 0.005 0.001 ARG A 532 Details of bonding type rmsd hydrogen bonds : bond 0.14982 ( 193) hydrogen bonds : angle 8.08867 ( 501) metal coordination : bond 0.18104 ( 7) covalent geometry : bond 0.00598 ( 7074) covalent geometry : angle 0.87531 ( 9613) *********************** 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 : 0.825 Fit side-chains revert: symmetry clash REVERT: A 36 ILE cc_start: 0.6943 (mm) cc_final: 0.6737 (mm) REVERT: A 48 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7706 (t0) REVERT: A 142 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8200 (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: 0.9602 time to fit residues: 98.0699 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 : 0.771 ------------------------------------------------------------------------------- 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 70 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.097920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.071824 restraints weight = 44018.101| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 4.37 r_work: 0.2792 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7081 Z= 0.152 Angle : 0.568 6.494 9613 Z= 0.314 Chirality : 0.044 0.169 1003 Planarity : 0.004 0.047 1252 Dihedral : 6.420 41.137 998 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.51 % Allowed : 13.59 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.25 (0.27), residues: 856 helix: 0.34 (0.45), residues: 136 sheet: 0.60 (0.40), residues: 154 loop : 0.07 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 223 HIS 0.008 0.002 HIS A 170 PHE 0.019 0.002 PHE A 524 TYR 0.022 0.002 TYR A 173 ARG 0.005 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 193) hydrogen bonds : angle 6.17470 ( 501) metal coordination : bond 0.00608 ( 7) covalent geometry : bond 0.00354 ( 7074) covalent geometry : angle 0.56762 ( 9613) *********************** 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 71 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.747 Fit side-chains REVERT: A 48 ASN cc_start: 0.7987 (OUTLIER) cc_final: 0.7500 (t0) REVERT: A 255 MET cc_start: 0.9079 (mmm) cc_final: 0.8716 (tpt) REVERT: A 322 ASN cc_start: 0.8011 (p0) cc_final: 0.7774 (p0) REVERT: A 658 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7102 (t0) REVERT: A 725 THR cc_start: 0.9108 (p) cc_final: 0.8788 (t) REVERT: A 745 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.7774 (t70) outliers start: 10 outliers final: 3 residues processed: 68 average time/residue: 0.9541 time to fit residues: 69.9972 Evaluate side-chains 48 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 476 CYS 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 10 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN B Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.092865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.067280 restraints weight = 65155.108| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 4.76 r_work: 0.2676 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 7081 Z= 0.259 Angle : 0.630 8.189 9613 Z= 0.344 Chirality : 0.047 0.209 1003 Planarity : 0.005 0.054 1252 Dihedral : 5.765 37.449 986 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.24 % Allowed : 14.91 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.10 (0.28), residues: 856 helix: 0.20 (0.45), residues: 135 sheet: 0.04 (0.38), residues: 170 loop : 0.15 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 579 HIS 0.007 0.002 HIS A 170 PHE 0.016 0.002 PHE A 510 TYR 0.028 0.002 TYR A 173 ARG 0.005 0.001 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 193) hydrogen bonds : angle 6.12019 ( 501) metal coordination : bond 0.00723 ( 7) covalent geometry : bond 0.00610 ( 7074) covalent geometry : angle 0.63011 ( 9613) *********************** 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 48 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.811 Fit side-chains REVERT: A 48 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7711 (t0) REVERT: A 255 MET cc_start: 0.9137 (mmm) cc_final: 0.8788 (tpt) REVERT: A 599 MET cc_start: 0.9130 (tpp) cc_final: 0.8900 (tpp) REVERT: A 725 THR cc_start: 0.9107 (p) cc_final: 0.8823 (t) REVERT: A 745 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8092 (t70) outliers start: 7 outliers final: 2 residues processed: 47 average time/residue: 1.0340 time to fit residues: 52.5609 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 : 0.766 ------------------------------------------------------------------------------- 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 745 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 2 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 60 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.095708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.070376 restraints weight = 60960.260| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.70 r_work: 0.2741 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7081 Z= 0.127 Angle : 0.530 9.370 9613 Z= 0.284 Chirality : 0.043 0.202 1003 Planarity : 0.004 0.038 1252 Dihedral : 5.095 36.323 984 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.11 % Allowed : 15.17 % 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 (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: 0.16 (0.28), residues: 856 helix: 0.47 (0.46), residues: 135 sheet: 0.38 (0.41), residues: 154 loop : 0.02 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 223 HIS 0.008 0.002 HIS A 170 PHE 0.015 0.001 PHE A 524 TYR 0.022 0.001 TYR A 173 ARG 0.004 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 193) hydrogen bonds : angle 5.80500 ( 501) metal coordination : bond 0.00321 ( 7) covalent geometry : bond 0.00300 ( 7074) covalent geometry : angle 0.53027 ( 9613) *********************** 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 52 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.851 Fit side-chains REVERT: A 48 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7630 (t0) REVERT: A 255 MET cc_start: 0.9065 (mmm) cc_final: 0.8752 (tpt) REVERT: A 658 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7342 (t0) REVERT: A 745 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8015 (t70) outliers start: 6 outliers final: 0 residues processed: 52 average time/residue: 1.0215 time to fit residues: 57.5083 Evaluate side-chains 43 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASN 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 10 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3292 r_free = 0.3292 target = 0.091804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.066396 restraints weight = 61731.404| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 4.68 r_work: 0.2669 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7081 Z= 0.273 Angle : 0.601 6.090 9613 Z= 0.326 Chirality : 0.047 0.247 1003 Planarity : 0.004 0.046 1252 Dihedral : 5.315 33.649 982 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.98 % Allowed : 16.23 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.03 (0.28), residues: 856 helix: 0.24 (0.46), residues: 136 sheet: -0.03 (0.37), residues: 176 loop : 0.08 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 340 HIS 0.007 0.002 HIS A 468 PHE 0.015 0.002 PHE A 287 TYR 0.027 0.002 TYR A 173 ARG 0.004 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 193) hydrogen bonds : angle 6.04562 ( 501) metal coordination : bond 0.00728 ( 7) covalent geometry : bond 0.00641 ( 7074) covalent geometry : angle 0.60114 ( 9613) *********************** 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 47 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.826 Fit side-chains REVERT: A 48 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7764 (t0) REVERT: A 255 MET cc_start: 0.9159 (mmm) cc_final: 0.8741 (tpt) REVERT: A 658 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7603 (t0) outliers start: 5 outliers final: 1 residues processed: 46 average time/residue: 1.0850 time to fit residues: 54.0519 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 : 0.841 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.5980 chunk 58 optimal weight: 0.0370 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.095681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.070121 restraints weight = 61087.064| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.77 r_work: 0.2741 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7081 Z= 0.117 Angle : 0.512 7.972 9613 Z= 0.275 Chirality : 0.043 0.243 1003 Planarity : 0.003 0.033 1252 Dihedral : 4.697 34.689 980 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.72 % Allowed : 16.62 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.08 (0.29), residues: 856 helix: 0.56 (0.47), residues: 135 sheet: -0.01 (0.38), residues: 176 loop : 0.04 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 223 HIS 0.007 0.002 HIS A 539 PHE 0.014 0.001 PHE A 524 TYR 0.022 0.001 TYR A 487 ARG 0.004 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 193) hydrogen bonds : angle 5.64600 ( 501) metal coordination : bond 0.00289 ( 7) covalent geometry : bond 0.00276 ( 7074) covalent geometry : angle 0.51186 ( 9613) *********************** 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 42 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.760 Fit side-chains REVERT: A 48 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7694 (t0) REVERT: A 255 MET cc_start: 0.9055 (mmm) cc_final: 0.8779 (tpt) REVERT: A 658 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7470 (t0) outliers start: 3 outliers final: 1 residues processed: 42 average time/residue: 0.9424 time to fit residues: 43.2274 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 : 0.795 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 71 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.094635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.069541 restraints weight = 58736.753| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 4.64 r_work: 0.2704 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3094 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= 0.166 Angle : 0.529 7.124 9613 Z= 0.285 Chirality : 0.043 0.241 1003 Planarity : 0.003 0.038 1252 Dihedral : 4.743 34.186 980 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.72 % Allowed : 16.89 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.10 (0.29), residues: 856 helix: 0.55 (0.47), residues: 135 sheet: -0.02 (0.38), residues: 175 loop : 0.06 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 579 HIS 0.006 0.002 HIS A 170 PHE 0.012 0.001 PHE A 524 TYR 0.024 0.002 TYR A 173 ARG 0.004 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 193) hydrogen bonds : angle 5.69657 ( 501) metal coordination : bond 0.00427 ( 7) covalent geometry : bond 0.00390 ( 7074) covalent geometry : angle 0.52945 ( 9613) *********************** 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 44 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.828 Fit side-chains REVERT: A 48 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7761 (t0) REVERT: A 255 MET cc_start: 0.9126 (mmm) cc_final: 0.8756 (tpt) REVERT: A 296 GLN cc_start: 0.8629 (tt0) cc_final: 0.8310 (tm-30) REVERT: A 658 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7489 (t0) outliers start: 4 outliers final: 2 residues processed: 43 average time/residue: 0.9975 time to fit residues: 46.8024 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 : 0.848 ------------------------------------------------------------------------------- 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 688 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 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 = 0.3339 r_free = 0.3339 target = 0.094809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.069481 restraints weight = 65294.449| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 4.79 r_work: 0.2723 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7081 Z= 0.135 Angle : 0.514 8.461 9613 Z= 0.275 Chirality : 0.043 0.240 1003 Planarity : 0.003 0.037 1252 Dihedral : 4.614 34.531 980 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.98 % Allowed : 16.49 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.29), residues: 856 helix: 0.61 (0.47), residues: 135 sheet: -0.00 (0.38), residues: 175 loop : 0.07 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 223 HIS 0.007 0.001 HIS A 539 PHE 0.013 0.001 PHE A 524 TYR 0.023 0.001 TYR A 173 ARG 0.004 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 193) hydrogen bonds : angle 5.60531 ( 501) metal coordination : bond 0.00329 ( 7) covalent geometry : bond 0.00318 ( 7074) covalent geometry : angle 0.51431 ( 9613) *********************** 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 47 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.816 Fit side-chains REVERT: A 48 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7727 (t0) REVERT: A 255 MET cc_start: 0.9112 (mmm) cc_final: 0.8752 (tpt) REVERT: A 296 GLN cc_start: 0.8613 (tt0) cc_final: 0.8356 (tm-30) REVERT: A 658 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7485 (t0) outliers start: 6 outliers final: 3 residues processed: 45 average time/residue: 0.9378 time to fit residues: 46.1714 Evaluate side-chains 45 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 688 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3287 r_free = 0.3287 target = 0.091304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.065817 restraints weight = 65100.570| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 4.77 r_work: 0.2656 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 7081 Z= 0.306 Angle : 0.610 6.652 9613 Z= 0.329 Chirality : 0.047 0.258 1003 Planarity : 0.004 0.047 1252 Dihedral : 5.110 33.977 980 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.85 % Allowed : 16.75 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.03 (0.29), residues: 856 helix: 0.13 (0.45), residues: 142 sheet: -0.14 (0.37), residues: 173 loop : 0.09 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 340 HIS 0.007 0.002 HIS A 468 PHE 0.019 0.002 PHE A 287 TYR 0.028 0.002 TYR A 173 ARG 0.005 0.001 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 193) hydrogen bonds : angle 5.97609 ( 501) metal coordination : bond 0.00778 ( 7) covalent geometry : bond 0.00717 ( 7074) covalent geometry : angle 0.60988 ( 9613) *********************** 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 44 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.884 Fit side-chains REVERT: A 48 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7838 (t0) REVERT: A 255 MET cc_start: 0.9187 (mmm) cc_final: 0.8787 (tpt) REVERT: A 658 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7600 (t0) outliers start: 5 outliers final: 2 residues processed: 43 average time/residue: 0.9949 time to fit residues: 46.7070 Evaluate side-chains 41 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 0.0970 chunk 58 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.0570 chunk 23 optimal weight: 0.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.095010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.069390 restraints weight = 71900.671| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 5.01 r_work: 0.2723 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- 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 = 0.04 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 = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7081 Z= 0.114 Angle : 0.517 8.427 9613 Z= 0.278 Chirality : 0.043 0.234 1003 Planarity : 0.003 0.040 1252 Dihedral : 4.729 34.801 980 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.72 % Allowed : 16.62 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.29), residues: 856 helix: 0.65 (0.48), residues: 129 sheet: -0.09 (0.38), residues: 179 loop : 0.12 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 223 HIS 0.006 0.001 HIS A 170 PHE 0.013 0.001 PHE A 524 TYR 0.022 0.001 TYR A 173 ARG 0.003 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.03108 ( 193) hydrogen bonds : angle 5.64702 ( 501) metal coordination : bond 0.00296 ( 7) covalent geometry : bond 0.00269 ( 7074) covalent geometry : angle 0.51738 ( 9613) ********************** 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 47 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.781 Fit side-chains REVERT: A 48 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7783 (t0) REVERT: A 255 MET cc_start: 0.9111 (mmm) cc_final: 0.8791 (tpt) REVERT: A 296 GLN cc_start: 0.8623 (tt0) cc_final: 0.8343 (tm-30) REVERT: A 658 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7521 (t0) outliers start: 4 outliers final: 2 residues processed: 46 average time/residue: 0.9792 time to fit residues: 49.0082 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 : 0.834 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 83 optimal weight: 0.0870 chunk 55 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 13 optimal weight: 0.4980 overall best weight: 1.2562 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.094307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.069164 restraints weight = 66211.774| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 4.82 r_work: 0.2694 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7081 Z= 0.181 Angle : 0.540 7.820 9613 Z= 0.289 Chirality : 0.044 0.241 1003 Planarity : 0.004 0.039 1252 Dihedral : 4.769 34.375 980 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.58 % Allowed : 16.89 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.11 (0.29), residues: 856 helix: 0.50 (0.47), residues: 135 sheet: -0.17 (0.38), residues: 178 loop : 0.16 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 579 HIS 0.006 0.002 HIS A 170 PHE 0.014 0.001 PHE A 287 TYR 0.024 0.002 TYR A 173 ARG 0.004 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 193) hydrogen bonds : angle 5.71126 ( 501) metal coordination : bond 0.00456 ( 7) covalent geometry : bond 0.00426 ( 7074) covalent geometry : angle 0.54008 ( 9613) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4794.42 seconds wall clock time: 82 minutes 39.10 seconds (4959.10 seconds total)