Starting phenix.real_space_refine on Wed Jun 26 01:22:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y95_39070/06_2024/8y95_39070_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y95_39070/06_2024/8y95_39070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y95_39070/06_2024/8y95_39070.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y95_39070/06_2024/8y95_39070.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y95_39070/06_2024/8y95_39070_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y95_39070/06_2024/8y95_39070_updated.pdb" } resolution = 3.24 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= 0.001 sd= 0.050 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: 6 Type Number sf(0) Gaussians S 40 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 6042 2.51 5 N 1406 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "D TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D ARG 341": "NH1" <-> "NH2" Residue "D ARG 440": "NH1" <-> "NH2" Residue "D ARG 442": "NH1" <-> "NH2" Residue "D ARG 500": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D ARG 587": "NH1" <-> "NH2" Residue "D ARG 604": "NH1" <-> "NH2" Residue "D ARG 607": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 9018 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4495 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 542} Chain: "D" Number of atoms: 4495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4495 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 542} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' CL': 1, ' NA': 1, 'E5E': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' CL': 1, ' NA': 1, 'E5E': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.38, per 1000 atoms: 0.60 Number of scatterers: 9018 At special positions: 0 Unit cell: (100.01, 107.31, 93.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 40 16.00 Na 2 11.00 O 1526 8.00 N 1406 7.00 C 6042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 0 sheets defined 69.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 62 through 73 Processing helix chain 'A' and resid 76 through 88 Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 91 through 120 removed outlier: 4.346A pdb=" N ILE A 96 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Proline residue: A 97 - end of helix Proline residue: A 108 - end of helix removed outlier: 4.414A pdb=" N ASN A 120 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 167 removed outlier: 3.751A pdb=" N LYS A 135 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY A 136 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL A 137 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A 141 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 142 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A 151 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 167 " --> pdb=" O PHE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 235 through 252 Processing helix chain 'A' and resid 262 through 281 removed outlier: 3.991A pdb=" N ALA A 267 " --> pdb=" O TRP A 264 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 268 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 285 through 294 removed outlier: 4.387A pdb=" N SER A 288 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN A 292 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 339 through 372 Processing helix chain 'A' and resid 386 through 397 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 401 through 434 Processing helix chain 'A' and resid 436 through 440 removed outlier: 3.824A pdb=" N ARG A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 436 through 440' Processing helix chain 'A' and resid 442 through 461 removed outlier: 4.237A pdb=" N PHE A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 493 removed outlier: 4.075A pdb=" N THR A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 471 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 509 Processing helix chain 'A' and resid 515 through 522 Processing helix chain 'A' and resid 524 through 538 Processing helix chain 'A' and resid 552 through 579 Proline residue: A 570 - end of helix Processing helix chain 'A' and resid 584 through 592 Processing helix chain 'A' and resid 598 through 602 removed outlier: 3.771A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 598 through 602' Processing helix chain 'A' and resid 611 through 615 Processing helix chain 'D' and resid 62 through 73 Processing helix chain 'D' and resid 76 through 88 Proline residue: D 83 - end of helix Processing helix chain 'D' and resid 91 through 120 removed outlier: 4.349A pdb=" N ILE D 96 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Proline residue: D 97 - end of helix Proline residue: D 108 - end of helix removed outlier: 4.418A pdb=" N ASN D 120 " --> pdb=" O GLY D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 167 removed outlier: 3.742A pdb=" N LYS D 135 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY D 136 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL D 137 " --> pdb=" O PHE D 134 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL D 141 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 142 " --> pdb=" O TYR D 139 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D 151 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE D 167 " --> pdb=" O PHE D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 209 through 215 Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 235 through 252 Processing helix chain 'D' and resid 262 through 281 removed outlier: 4.010A pdb=" N ALA D 267 " --> pdb=" O TRP D 264 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR D 268 " --> pdb=" O ILE D 265 " (cutoff:3.500A) Proline residue: D 270 - end of helix Processing helix chain 'D' and resid 285 through 294 removed outlier: 4.386A pdb=" N SER D 288 " --> pdb=" O PRO D 285 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN D 292 " --> pdb=" O ASN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 319 Processing helix chain 'D' and resid 325 through 331 Processing helix chain 'D' and resid 339 through 372 Processing helix chain 'D' and resid 386 through 397 Proline residue: D 392 - end of helix Processing helix chain 'D' and resid 401 through 434 Processing helix chain 'D' and resid 436 through 440 removed outlier: 3.832A pdb=" N ARG D 440 " --> pdb=" O GLN D 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 436 through 440' Processing helix chain 'D' and resid 442 through 461 removed outlier: 4.250A pdb=" N PHE D 447 " --> pdb=" O LYS D 443 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 493 removed outlier: 4.086A pdb=" N THR D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU D 471 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 509 Processing helix chain 'D' and resid 515 through 522 Processing helix chain 'D' and resid 524 through 538 Processing helix chain 'D' and resid 552 through 579 Proline residue: D 570 - end of helix Processing helix chain 'D' and resid 584 through 592 Processing helix chain 'D' and resid 598 through 602 removed outlier: 3.772A pdb=" N ALA D 602 " --> pdb=" O HIS D 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 598 through 602' Processing helix chain 'D' and resid 611 through 615 518 hydrogen bonds defined for protein. 1182 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: 2.56 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2646 1.34 - 1.46: 2361 1.46 - 1.58: 4237 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 9306 Sorted by residual: bond pdb=" CAJ E5E D 701 " pdb=" OAC E5E D 701 " ideal model delta sigma weight residual 1.350 1.401 -0.051 2.00e-02 2.50e+03 6.51e+00 bond pdb=" CAJ E5E A 701 " pdb=" OAC E5E A 701 " ideal model delta sigma weight residual 1.350 1.394 -0.044 2.00e-02 2.50e+03 4.93e+00 bond pdb=" CAI E5E A 701 " pdb=" OAB E5E A 701 " ideal model delta sigma weight residual 1.354 1.395 -0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" CAI E5E D 701 " pdb=" OAB E5E D 701 " ideal model delta sigma weight residual 1.354 1.394 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" CAI E5E A 701 " pdb=" CAJ E5E A 701 " ideal model delta sigma weight residual 1.401 1.364 0.037 2.00e-02 2.50e+03 3.48e+00 ... (remaining 9301 not shown) Histogram of bond angle deviations from ideal: 100.75 - 107.40: 301 107.40 - 114.05: 5161 114.05 - 120.70: 4186 120.70 - 127.35: 2908 127.35 - 134.00: 140 Bond angle restraints: 12696 Sorted by residual: angle pdb=" C ASP A 546 " pdb=" CA ASP A 546 " pdb=" CB ASP A 546 " ideal model delta sigma weight residual 110.92 115.72 -4.80 1.59e+00 3.96e-01 9.11e+00 angle pdb=" C ASP D 546 " pdb=" CA ASP D 546 " pdb=" CB ASP D 546 " ideal model delta sigma weight residual 110.92 115.68 -4.76 1.59e+00 3.96e-01 8.98e+00 angle pdb=" N GLY D 231 " pdb=" CA GLY D 231 " pdb=" C GLY D 231 " ideal model delta sigma weight residual 111.21 114.29 -3.08 1.04e+00 9.25e-01 8.75e+00 angle pdb=" N GLY A 231 " pdb=" CA GLY A 231 " pdb=" C GLY A 231 " ideal model delta sigma weight residual 111.21 114.27 -3.06 1.04e+00 9.25e-01 8.65e+00 angle pdb=" C GLY D 106 " pdb=" N MET D 107 " pdb=" CA MET D 107 " ideal model delta sigma weight residual 121.80 114.95 6.85 2.44e+00 1.68e-01 7.89e+00 ... (remaining 12691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4918 17.89 - 35.77: 210 35.77 - 53.66: 56 53.66 - 71.55: 6 71.55 - 89.43: 6 Dihedral angle restraints: 5196 sinusoidal: 1950 harmonic: 3246 Sorted by residual: dihedral pdb=" CA THR D 268 " pdb=" C THR D 268 " pdb=" N LEU D 269 " pdb=" CA LEU D 269 " ideal model delta harmonic sigma weight residual -180.00 -160.60 -19.40 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA THR A 268 " pdb=" C THR A 268 " pdb=" N LEU A 269 " pdb=" CA LEU A 269 " ideal model delta harmonic sigma weight residual 180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA SER A 493 " pdb=" C SER A 493 " pdb=" N TRP A 494 " pdb=" CA TRP A 494 " ideal model delta harmonic sigma weight residual 180.00 -164.36 -15.64 0 5.00e+00 4.00e-02 9.78e+00 ... (remaining 5193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1046 0.036 - 0.072: 304 0.072 - 0.108: 52 0.108 - 0.145: 9 0.145 - 0.181: 3 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CAL E5E D 701 " pdb=" CAH E5E D 701 " pdb=" CAK E5E D 701 " pdb=" OAD E5E D 701 " both_signs ideal model delta sigma weight residual False -2.31 -2.49 0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA LEU A 269 " pdb=" N LEU A 269 " pdb=" C LEU A 269 " pdb=" CB LEU A 269 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA LEU D 269 " pdb=" N LEU D 269 " pdb=" C LEU D 269 " pdb=" CB LEU D 269 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 1411 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 477 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.73e+00 pdb=" C ALA A 477 " -0.051 2.00e-02 2.50e+03 pdb=" O ALA A 477 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY A 478 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 477 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C ALA D 477 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA D 477 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY D 478 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 481 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C ILE D 481 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE D 481 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU D 482 " -0.016 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 2 2.10 - 2.80: 2621 2.80 - 3.50: 13275 3.50 - 4.20: 21756 4.20 - 4.90: 39370 Nonbonded interactions: 77024 Sorted by model distance: nonbonded pdb=" OD1 ASN A 78 " pdb="NA NA A 703 " model vdw 1.402 2.470 nonbonded pdb=" OD1 ASN A 350 " pdb="NA NA A 703 " model vdw 2.088 2.470 nonbonded pdb=" OH TYR D 98 " pdb="CL CL D 702 " model vdw 2.113 2.590 nonbonded pdb=" O ALA A 145 " pdb=" OAB E5E A 701 " model vdw 2.149 2.440 nonbonded pdb=" OH TYR A 98 " pdb="CL CL A 702 " model vdw 2.161 2.590 ... (remaining 77019 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 7.000 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.670 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 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 : 0.003 0.051 9306 Z= 0.155 Angle : 0.589 8.585 12696 Z= 0.342 Chirality : 0.036 0.181 1414 Planarity : 0.006 0.060 1544 Dihedral : 11.301 89.435 3132 Min Nonbonded Distance : 1.402 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.43 % Allowed : 6.75 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.23), residues: 1120 helix: -0.91 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -1.73 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS D 228 PHE 0.014 0.001 PHE D 65 TYR 0.024 0.001 TYR D 151 ARG 0.002 0.000 ARG D 442 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 278 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8294 (m-10) REVERT: A 303 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7796 (mmtt) REVERT: A 377 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6497 (mm-30) REVERT: A 519 LEU cc_start: 0.8096 (mt) cc_final: 0.7734 (mt) REVERT: A 544 THR cc_start: 0.7115 (t) cc_final: 0.6758 (t) REVERT: A 548 TYR cc_start: 0.7364 (t80) cc_final: 0.6795 (t80) REVERT: A 563 LEU cc_start: 0.7006 (mt) cc_final: 0.6767 (mt) REVERT: A 615 LEU cc_start: 0.8194 (tt) cc_final: 0.7948 (mt) REVERT: D 107 MET cc_start: 0.4599 (OUTLIER) cc_final: 0.3819 (mpp) REVERT: D 120 ASN cc_start: 0.8215 (m-40) cc_final: 0.7924 (m110) REVERT: D 133 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8295 (m-10) REVERT: D 303 LYS cc_start: 0.8225 (mtmt) cc_final: 0.7778 (mmtt) REVERT: D 377 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6568 (mm-30) REVERT: D 515 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7112 (tp) REVERT: D 519 LEU cc_start: 0.8130 (mt) cc_final: 0.7787 (mt) REVERT: D 544 THR cc_start: 0.7061 (t) cc_final: 0.6708 (t) REVERT: D 548 TYR cc_start: 0.7356 (t80) cc_final: 0.6860 (t80) REVERT: D 563 LEU cc_start: 0.7028 (mt) cc_final: 0.6783 (mt) REVERT: D 615 LEU cc_start: 0.8209 (tt) cc_final: 0.7971 (mt) outliers start: 42 outliers final: 6 residues processed: 309 average time/residue: 0.2056 time to fit residues: 87.4608 Evaluate side-chains 172 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 515 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0370 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN A 280 HIS A 333 ASN A 581 GLN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN D 89 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN D 280 HIS D 333 ASN ** D 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN D 613 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9306 Z= 0.185 Angle : 0.566 7.725 12696 Z= 0.294 Chirality : 0.039 0.160 1414 Planarity : 0.005 0.055 1544 Dihedral : 5.568 49.803 1245 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.54 % Allowed : 13.61 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1120 helix: -0.04 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -1.17 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 553 HIS 0.016 0.001 HIS A 598 PHE 0.031 0.001 PHE D 359 TYR 0.017 0.002 TYR A 151 ARG 0.006 0.001 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 176 time to evaluate : 1.115 Fit side-chains REVERT: A 133 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8360 (m-80) REVERT: A 189 LYS cc_start: 0.6906 (ttpt) cc_final: 0.6609 (tptt) REVERT: A 303 LYS cc_start: 0.8263 (mtmt) cc_final: 0.7752 (mmtt) REVERT: A 377 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6560 (mm-30) REVERT: A 519 LEU cc_start: 0.8164 (mt) cc_final: 0.7952 (mt) REVERT: A 548 TYR cc_start: 0.7616 (t80) cc_final: 0.6945 (t80) REVERT: A 563 LEU cc_start: 0.7300 (mt) cc_final: 0.7058 (mt) REVERT: A 615 LEU cc_start: 0.8179 (tt) cc_final: 0.7944 (mt) REVERT: D 107 MET cc_start: 0.4756 (OUTLIER) cc_final: 0.3618 (mpp) REVERT: D 133 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: D 303 LYS cc_start: 0.8264 (mtmt) cc_final: 0.7747 (mmtt) REVERT: D 377 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6589 (mm-30) REVERT: D 517 TRP cc_start: 0.7398 (m100) cc_final: 0.7185 (m100) REVERT: D 519 LEU cc_start: 0.8238 (mt) cc_final: 0.8002 (mt) REVERT: D 548 TYR cc_start: 0.7611 (t80) cc_final: 0.6981 (t80) REVERT: D 563 LEU cc_start: 0.7332 (mt) cc_final: 0.7056 (mt) REVERT: D 615 LEU cc_start: 0.8230 (tt) cc_final: 0.7984 (mt) outliers start: 43 outliers final: 23 residues processed: 208 average time/residue: 0.1738 time to fit residues: 52.7829 Evaluate side-chains 182 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 534 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 HIS A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 ASN ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 9306 Z= 0.340 Angle : 0.689 11.280 12696 Z= 0.355 Chirality : 0.045 0.217 1414 Planarity : 0.006 0.050 1544 Dihedral : 5.689 49.845 1235 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.70 % Allowed : 15.82 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.25), residues: 1120 helix: -0.01 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -0.80 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 559 HIS 0.006 0.001 HIS D 599 PHE 0.024 0.002 PHE D 213 TYR 0.021 0.002 TYR A 572 ARG 0.005 0.001 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 173 time to evaluate : 1.099 Fit side-chains REVERT: A 88 LYS cc_start: 0.8786 (pttt) cc_final: 0.8515 (ptpt) REVERT: A 107 MET cc_start: 0.6207 (mpp) cc_final: 0.5899 (mmt) REVERT: A 133 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: A 189 LYS cc_start: 0.7163 (ttpt) cc_final: 0.6765 (tptt) REVERT: A 377 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6901 (mm-30) REVERT: A 615 LEU cc_start: 0.8400 (tt) cc_final: 0.8092 (mt) REVERT: D 88 LYS cc_start: 0.8762 (pttt) cc_final: 0.8523 (ptpt) REVERT: D 133 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8450 (m-80) REVERT: D 189 LYS cc_start: 0.7018 (ttpt) cc_final: 0.6787 (tptt) REVERT: D 303 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7793 (mmtt) REVERT: D 377 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6909 (mm-30) REVERT: D 540 PHE cc_start: 0.8942 (t80) cc_final: 0.8706 (t80) REVERT: D 615 LEU cc_start: 0.8376 (tt) cc_final: 0.8092 (mt) outliers start: 54 outliers final: 37 residues processed: 208 average time/residue: 0.1865 time to fit residues: 56.3017 Evaluate side-chains 187 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 148 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 579 SER Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain D residue 601 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0370 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 0.0030 overall best weight: 0.4668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN D 153 ASN D 198 ASN ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9306 Z= 0.170 Angle : 0.545 10.656 12696 Z= 0.280 Chirality : 0.038 0.133 1414 Planarity : 0.005 0.051 1544 Dihedral : 5.382 51.373 1235 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.01 % Allowed : 19.41 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.25), residues: 1120 helix: 0.20 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -0.52 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 517 HIS 0.006 0.001 HIS D 599 PHE 0.014 0.001 PHE D 65 TYR 0.014 0.001 TYR D 516 ARG 0.005 0.001 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8397 (m-80) REVERT: A 189 LYS cc_start: 0.7037 (ttpt) cc_final: 0.6687 (tptt) REVERT: A 332 TYR cc_start: 0.8264 (m-80) cc_final: 0.7968 (m-80) REVERT: A 377 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6816 (mm-30) REVERT: A 615 LEU cc_start: 0.8293 (tt) cc_final: 0.8016 (mt) REVERT: D 133 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: D 189 LYS cc_start: 0.6954 (ttpt) cc_final: 0.6699 (tptt) REVERT: D 303 LYS cc_start: 0.8343 (mtmt) cc_final: 0.7757 (mmtt) REVERT: D 332 TYR cc_start: 0.8327 (m-80) cc_final: 0.8038 (m-80) REVERT: D 377 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6853 (mm-30) REVERT: D 540 PHE cc_start: 0.8903 (t80) cc_final: 0.8683 (t80) REVERT: D 615 LEU cc_start: 0.8266 (tt) cc_final: 0.8011 (mt) outliers start: 38 outliers final: 23 residues processed: 179 average time/residue: 0.1790 time to fit residues: 46.1553 Evaluate side-chains 169 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 598 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 97 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9306 Z= 0.195 Angle : 0.551 9.306 12696 Z= 0.280 Chirality : 0.038 0.130 1414 Planarity : 0.005 0.051 1544 Dihedral : 4.956 43.526 1228 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.85 % Allowed : 19.09 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1120 helix: 0.42 (0.20), residues: 724 sheet: None (None), residues: 0 loop : -0.66 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 517 HIS 0.005 0.001 HIS D 599 PHE 0.031 0.001 PHE A 213 TYR 0.013 0.001 TYR A 572 ARG 0.003 0.000 ARG D 604 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 138 time to evaluate : 0.988 Fit side-chains REVERT: A 133 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8416 (m-80) REVERT: A 189 LYS cc_start: 0.7065 (ttpt) cc_final: 0.6713 (tptt) REVERT: A 377 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6807 (mm-30) REVERT: A 615 LEU cc_start: 0.8268 (tt) cc_final: 0.8007 (mt) REVERT: D 122 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7287 (mp0) REVERT: D 133 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: D 189 LYS cc_start: 0.6983 (ttpt) cc_final: 0.6648 (tptt) REVERT: D 303 LYS cc_start: 0.8363 (mtmt) cc_final: 0.7749 (mmtt) REVERT: D 377 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6901 (mm-30) REVERT: D 540 PHE cc_start: 0.8903 (t80) cc_final: 0.8625 (t80) REVERT: D 615 LEU cc_start: 0.8243 (tt) cc_final: 0.7988 (mt) outliers start: 46 outliers final: 33 residues processed: 176 average time/residue: 0.1735 time to fit residues: 44.4066 Evaluate side-chains 172 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 137 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 579 SER Chi-restraints excluded: chain D residue 598 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 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 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9306 Z= 0.206 Angle : 0.553 10.051 12696 Z= 0.282 Chirality : 0.038 0.134 1414 Planarity : 0.005 0.047 1544 Dihedral : 5.001 45.677 1228 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.06 % Allowed : 18.99 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1120 helix: 0.45 (0.20), residues: 726 sheet: None (None), residues: 0 loop : -0.45 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 517 HIS 0.005 0.001 HIS D 599 PHE 0.016 0.001 PHE A 213 TYR 0.013 0.001 TYR D 572 ARG 0.004 0.001 ARG D 604 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 136 time to evaluate : 0.918 Fit side-chains REVERT: A 122 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7245 (mp0) REVERT: A 133 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: A 189 LYS cc_start: 0.7075 (ttpt) cc_final: 0.6707 (tptt) REVERT: A 377 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6889 (mm-30) REVERT: A 471 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6129 (tp) REVERT: A 596 ASN cc_start: 0.7579 (p0) cc_final: 0.7341 (p0) REVERT: A 615 LEU cc_start: 0.8265 (tt) cc_final: 0.8008 (mt) REVERT: D 122 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7280 (mp0) REVERT: D 133 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8417 (m-80) REVERT: D 189 LYS cc_start: 0.7015 (ttpt) cc_final: 0.6659 (tptt) REVERT: D 377 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6885 (mm-30) REVERT: D 615 LEU cc_start: 0.8254 (tt) cc_final: 0.8003 (mt) outliers start: 48 outliers final: 35 residues processed: 174 average time/residue: 0.1758 time to fit residues: 44.5868 Evaluate side-chains 169 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 131 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 579 SER Chi-restraints excluded: chain D residue 598 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 10.0000 chunk 61 optimal weight: 0.4980 chunk 79 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.0270 chunk 107 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.0370 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9306 Z= 0.167 Angle : 0.539 9.616 12696 Z= 0.272 Chirality : 0.037 0.164 1414 Planarity : 0.005 0.045 1544 Dihedral : 4.896 44.048 1228 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.32 % Allowed : 19.73 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1120 helix: 0.42 (0.20), residues: 734 sheet: None (None), residues: 0 loop : -0.27 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 517 HIS 0.005 0.001 HIS D 599 PHE 0.014 0.001 PHE A 213 TYR 0.011 0.001 TYR D 84 ARG 0.006 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 132 time to evaluate : 0.889 Fit side-chains REVERT: A 122 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7317 (mp0) REVERT: A 133 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8409 (m-80) REVERT: A 189 LYS cc_start: 0.6989 (ttpt) cc_final: 0.6639 (tptt) REVERT: A 332 TYR cc_start: 0.8485 (m-80) cc_final: 0.8085 (m-80) REVERT: A 342 ASP cc_start: 0.8103 (t0) cc_final: 0.7734 (t0) REVERT: A 377 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6779 (mm-30) REVERT: A 424 MET cc_start: 0.7836 (mmm) cc_final: 0.7535 (mtp) REVERT: A 444 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8217 (tt) REVERT: A 596 ASN cc_start: 0.7519 (p0) cc_final: 0.7305 (p0) REVERT: A 615 LEU cc_start: 0.8218 (tt) cc_final: 0.7975 (mt) REVERT: D 122 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7288 (mp0) REVERT: D 133 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: D 189 LYS cc_start: 0.7013 (ttpt) cc_final: 0.6676 (tptt) REVERT: D 332 TYR cc_start: 0.8382 (m-80) cc_final: 0.8022 (m-80) REVERT: D 342 ASP cc_start: 0.8053 (t0) cc_final: 0.7685 (t0) REVERT: D 377 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6782 (mm-30) REVERT: D 615 LEU cc_start: 0.8203 (tt) cc_final: 0.7974 (mt) outliers start: 41 outliers final: 33 residues processed: 162 average time/residue: 0.1726 time to fit residues: 40.6340 Evaluate side-chains 166 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 130 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 598 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 0.0870 chunk 98 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS A 289 ASN ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9306 Z= 0.237 Angle : 0.582 10.583 12696 Z= 0.295 Chirality : 0.039 0.144 1414 Planarity : 0.005 0.044 1544 Dihedral : 5.071 46.753 1228 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.17 % Allowed : 19.51 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1120 helix: 0.44 (0.20), residues: 726 sheet: None (None), residues: 0 loop : -0.39 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 517 HIS 0.006 0.001 HIS A 220 PHE 0.015 0.001 PHE D 65 TYR 0.022 0.001 TYR D 367 ARG 0.003 0.000 ARG D 604 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 129 time to evaluate : 0.966 Fit side-chains REVERT: A 133 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: A 189 LYS cc_start: 0.7072 (ttpt) cc_final: 0.6650 (tptt) REVERT: A 332 TYR cc_start: 0.8535 (m-80) cc_final: 0.8203 (m-80) REVERT: A 342 ASP cc_start: 0.8151 (t0) cc_final: 0.7732 (t0) REVERT: A 377 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6909 (mm-30) REVERT: A 424 MET cc_start: 0.7768 (mmm) cc_final: 0.7414 (mtt) REVERT: A 615 LEU cc_start: 0.8296 (tt) cc_final: 0.8031 (mt) REVERT: D 133 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: D 189 LYS cc_start: 0.7077 (ttpt) cc_final: 0.6658 (tptt) REVERT: D 332 TYR cc_start: 0.8467 (m-80) cc_final: 0.8201 (m-80) REVERT: D 377 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6936 (mm-30) REVERT: D 424 MET cc_start: 0.7682 (mmm) cc_final: 0.7212 (mtt) REVERT: D 615 LEU cc_start: 0.8312 (tt) cc_final: 0.8068 (mt) outliers start: 49 outliers final: 40 residues processed: 168 average time/residue: 0.1723 time to fit residues: 42.6247 Evaluate side-chains 166 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 124 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 579 SER Chi-restraints excluded: chain D residue 598 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 0.0370 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9306 Z= 0.179 Angle : 0.562 9.947 12696 Z= 0.282 Chirality : 0.038 0.137 1414 Planarity : 0.005 0.046 1544 Dihedral : 5.016 45.522 1228 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.64 % Allowed : 20.15 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1120 helix: 0.40 (0.19), residues: 734 sheet: None (None), residues: 0 loop : -0.21 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 517 HIS 0.004 0.001 HIS D 599 PHE 0.014 0.001 PHE D 65 TYR 0.019 0.001 TYR D 367 ARG 0.005 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 132 time to evaluate : 1.189 Fit side-chains REVERT: A 133 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8397 (m-80) REVERT: A 189 LYS cc_start: 0.7010 (ttpt) cc_final: 0.6627 (tptt) REVERT: A 190 LEU cc_start: 0.7783 (tp) cc_final: 0.7477 (tp) REVERT: A 332 TYR cc_start: 0.8560 (m-80) cc_final: 0.8271 (m-80) REVERT: A 342 ASP cc_start: 0.8111 (t0) cc_final: 0.7723 (t0) REVERT: A 377 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6855 (mm-30) REVERT: A 424 MET cc_start: 0.7781 (mmm) cc_final: 0.7437 (mtt) REVERT: A 615 LEU cc_start: 0.8268 (tt) cc_final: 0.8013 (mt) REVERT: D 122 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7239 (mp0) REVERT: D 133 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: D 189 LYS cc_start: 0.7022 (ttpt) cc_final: 0.6626 (tptt) REVERT: D 332 TYR cc_start: 0.8445 (m-80) cc_final: 0.8229 (m-80) REVERT: D 342 ASP cc_start: 0.8063 (t0) cc_final: 0.7688 (t0) REVERT: D 377 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6924 (mm-30) REVERT: D 424 MET cc_start: 0.7656 (mmm) cc_final: 0.7210 (mtt) REVERT: D 615 LEU cc_start: 0.8259 (tt) cc_final: 0.8029 (mt) outliers start: 44 outliers final: 35 residues processed: 166 average time/residue: 0.1744 time to fit residues: 42.5336 Evaluate side-chains 167 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 598 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 ASN D 555 ASN ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9306 Z= 0.213 Angle : 0.583 10.325 12696 Z= 0.292 Chirality : 0.039 0.159 1414 Planarity : 0.005 0.046 1544 Dihedral : 5.108 47.642 1228 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.43 % Allowed : 20.57 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1120 helix: 0.37 (0.19), residues: 732 sheet: None (None), residues: 0 loop : -0.22 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 517 HIS 0.004 0.001 HIS D 599 PHE 0.014 0.001 PHE D 65 TYR 0.018 0.001 TYR D 367 ARG 0.005 0.000 ARG A 604 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 130 time to evaluate : 0.902 Fit side-chains REVERT: A 133 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8457 (m-80) REVERT: A 189 LYS cc_start: 0.7011 (ttpt) cc_final: 0.6616 (tptt) REVERT: A 190 LEU cc_start: 0.7839 (tp) cc_final: 0.7602 (tp) REVERT: A 332 TYR cc_start: 0.8578 (m-80) cc_final: 0.8293 (m-80) REVERT: A 342 ASP cc_start: 0.8146 (t0) cc_final: 0.7742 (t0) REVERT: A 377 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6965 (mm-30) REVERT: A 424 MET cc_start: 0.7745 (mmm) cc_final: 0.7436 (mtt) REVERT: A 615 LEU cc_start: 0.8309 (tt) cc_final: 0.8052 (mt) REVERT: D 122 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7199 (mp0) REVERT: D 133 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8416 (m-80) REVERT: D 189 LYS cc_start: 0.7017 (ttpt) cc_final: 0.6591 (tptt) REVERT: D 190 LEU cc_start: 0.7799 (tp) cc_final: 0.7517 (tp) REVERT: D 332 TYR cc_start: 0.8480 (m-80) cc_final: 0.8270 (m-80) REVERT: D 342 ASP cc_start: 0.8089 (t0) cc_final: 0.7704 (t0) REVERT: D 377 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7002 (mm-30) REVERT: D 424 MET cc_start: 0.7686 (mmm) cc_final: 0.7257 (mtt) REVERT: D 615 LEU cc_start: 0.8316 (tt) cc_final: 0.8068 (mt) outliers start: 42 outliers final: 36 residues processed: 163 average time/residue: 0.1790 time to fit residues: 42.6107 Evaluate side-chains 164 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 126 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 280 HIS Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 598 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.171984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.138598 restraints weight = 12352.700| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.41 r_work: 0.3572 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9306 Z= 0.194 Angle : 0.573 10.185 12696 Z= 0.287 Chirality : 0.038 0.160 1414 Planarity : 0.005 0.046 1544 Dihedral : 5.082 47.079 1228 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.22 % Allowed : 20.68 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1120 helix: 0.41 (0.19), residues: 732 sheet: None (None), residues: 0 loop : -0.15 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 517 HIS 0.004 0.001 HIS D 599 PHE 0.014 0.001 PHE D 65 TYR 0.017 0.001 TYR D 367 ARG 0.005 0.000 ARG A 604 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2142.12 seconds wall clock time: 38 minutes 53.02 seconds (2333.02 seconds total)