Starting phenix.real_space_refine on Thu Mar 14 17:43:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psm_13614/03_2024/7psm_13614_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psm_13614/03_2024/7psm_13614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psm_13614/03_2024/7psm_13614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psm_13614/03_2024/7psm_13614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psm_13614/03_2024/7psm_13614_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psm_13614/03_2024/7psm_13614_updated.pdb" } resolution = 3.4 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= 0.096 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 P 8 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 6038 2.51 5 N 1602 2.21 5 O 1710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A GLU 528": "OE1" <-> "OE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B GLU 598": "OE1" <-> "OE2" Residue "B GLU 608": "OE1" <-> "OE2" Residue "B GLU 658": "OE1" <-> "OE2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B GLU 675": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9394 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4622 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 17, 'TRANS': 567} Chain: "B" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4622 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 17, 'TRANS': 567} Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 5.39, per 1000 atoms: 0.57 Number of scatterers: 9394 At special positions: 0 Unit cell: (82.467, 77.469, 141.61, 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) S 34 16.00 P 8 15.00 Mg 2 11.99 O 1710 8.00 N 1602 7.00 C 6038 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=0, symmetry=0 Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.8 seconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 4 sheets defined 61.0% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 105 through 139 Proline residue: A 129 - end of helix removed outlier: 3.598A pdb=" N MET A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 199 removed outlier: 3.996A pdb=" N THR A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 211 through 234 Processing helix chain 'A' and resid 236 through 253 Processing helix chain 'A' and resid 257 through 303 removed outlier: 5.370A pdb=" N HIS A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N PHE A 283 " --> pdb=" O TRP A 279 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 314 through 366 removed outlier: 4.052A pdb=" N SER A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 395 Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 575 through 589 Processing helix chain 'A' and resid 605 through 616 Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 666 through 675 Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 105 through 139 Proline residue: B 129 - end of helix removed outlier: 3.593A pdb=" N MET B 139 " --> pdb=" O THR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 199 removed outlier: 4.022A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 211 through 234 Processing helix chain 'B' and resid 236 through 253 Processing helix chain 'B' and resid 257 through 303 removed outlier: 5.371A pdb=" N HIS B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE B 283 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 284 " --> pdb=" O ARG B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 314 through 366 removed outlier: 4.052A pdb=" N SER B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 395 Proline residue: B 388 - end of helix Processing helix chain 'B' and resid 400 through 413 Processing helix chain 'B' and resid 476 through 482 Processing helix chain 'B' and resid 505 through 509 Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 539 through 548 Processing helix chain 'B' and resid 552 through 557 Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 575 through 589 Processing helix chain 'B' and resid 605 through 616 Processing helix chain 'B' and resid 656 through 660 Processing helix chain 'B' and resid 666 through 675 Processing sheet with id= A, first strand: chain 'A' and resid 457 through 459 Processing sheet with id= B, first strand: chain 'A' and resid 641 through 645 Processing sheet with id= C, first strand: chain 'B' and resid 457 through 459 Processing sheet with id= D, first strand: chain 'B' and resid 641 through 645 552 hydrogen bonds defined for protein. 1638 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: 2.48 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 1496 1.29 - 1.42: 2402 1.42 - 1.55: 5589 1.55 - 1.68: 13 1.68 - 1.81: 68 Bond restraints: 9568 Sorted by residual: bond pdb=" C3' ANP B 701 " pdb=" C4' ANP B 701 " ideal model delta sigma weight residual 1.532 1.308 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C3' ANP A 701 " pdb=" C4' ANP A 701 " ideal model delta sigma weight residual 1.532 1.309 0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C4' ANP A 701 " pdb=" O4' ANP A 701 " ideal model delta sigma weight residual 1.431 1.623 -0.192 2.00e-02 2.50e+03 9.21e+01 bond pdb=" C4' ANP B 701 " pdb=" O4' ANP B 701 " ideal model delta sigma weight residual 1.431 1.623 -0.192 2.00e-02 2.50e+03 9.19e+01 bond pdb=" C6 ANP B 701 " pdb=" N6 ANP B 701 " ideal model delta sigma weight residual 1.340 1.474 -0.134 2.00e-02 2.50e+03 4.51e+01 ... (remaining 9563 not shown) Histogram of bond angle deviations from ideal: 99.24 - 107.22: 253 107.22 - 115.20: 5881 115.20 - 123.17: 6442 123.17 - 131.15: 328 131.15 - 139.13: 38 Bond angle restraints: 12942 Sorted by residual: angle pdb=" C1' ANP A 701 " pdb=" N9 ANP A 701 " pdb=" C4 ANP A 701 " ideal model delta sigma weight residual 125.38 111.09 14.29 3.00e+00 1.11e-01 2.27e+01 angle pdb=" C1' ANP B 701 " pdb=" N9 ANP B 701 " pdb=" C4 ANP B 701 " ideal model delta sigma weight residual 125.38 111.10 14.28 3.00e+00 1.11e-01 2.27e+01 angle pdb=" O3 LOP A 703 " pdb=" P1 LOP A 703 " pdb=" O4 LOP A 703 " ideal model delta sigma weight residual 120.67 108.32 12.35 3.00e+00 1.11e-01 1.69e+01 angle pdb=" O3 LOP B 703 " pdb=" P1 LOP B 703 " pdb=" O4 LOP B 703 " ideal model delta sigma weight residual 120.67 108.34 12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C ARG B 188 " pdb=" CA ARG B 188 " pdb=" CB ARG B 188 " ideal model delta sigma weight residual 110.88 104.55 6.33 1.57e+00 4.06e-01 1.63e+01 ... (remaining 12937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.22: 5401 26.22 - 52.44: 318 52.44 - 78.66: 61 78.66 - 104.89: 8 104.89 - 131.11: 2 Dihedral angle restraints: 5790 sinusoidal: 2406 harmonic: 3384 Sorted by residual: dihedral pdb=" O1A ANP A 701 " pdb=" O3A ANP A 701 " pdb=" PA ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sinusoidal sigma weight residual 83.11 -48.00 131.11 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" O1A ANP B 701 " pdb=" O3A ANP B 701 " pdb=" PA ANP B 701 " pdb=" PB ANP B 701 " ideal model delta sinusoidal sigma weight residual 83.11 -47.95 131.06 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C VAL B 128 " pdb=" N VAL B 128 " pdb=" CA VAL B 128 " pdb=" CB VAL B 128 " ideal model delta harmonic sigma weight residual -122.00 -131.14 9.14 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 5787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1127 0.054 - 0.109: 300 0.109 - 0.163: 57 0.163 - 0.217: 6 0.217 - 0.272: 4 Chirality restraints: 1494 Sorted by residual: chirality pdb=" CB ILE B 419 " pdb=" CA ILE B 419 " pdb=" CG1 ILE B 419 " pdb=" CG2 ILE B 419 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE A 419 " pdb=" CA ILE A 419 " pdb=" CG1 ILE A 419 " pdb=" CG2 ILE A 419 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB VAL B 128 " pdb=" CA VAL B 128 " pdb=" CG1 VAL B 128 " pdb=" CG2 VAL B 128 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1491 not shown) Planarity restraints: 1616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 594 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C MET B 594 " 0.034 2.00e-02 2.50e+03 pdb=" O MET B 594 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE B 595 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 594 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C MET A 594 " -0.034 2.00e-02 2.50e+03 pdb=" O MET A 594 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE A 595 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 376 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C VAL A 376 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL A 376 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU A 377 " 0.011 2.00e-02 2.50e+03 ... (remaining 1613 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 104 2.64 - 3.21: 8257 3.21 - 3.77: 14720 3.77 - 4.34: 19064 4.34 - 4.90: 32115 Nonbonded interactions: 74260 Sorted by model distance: nonbonded pdb=" O2B ANP A 701 " pdb="MG MG A 702 " model vdw 2.078 2.170 nonbonded pdb=" O2B ANP B 701 " pdb="MG MG B 702 " model vdw 2.079 2.170 nonbonded pdb=" O3G ANP A 701 " pdb="MG MG A 702 " model vdw 2.093 2.170 nonbonded pdb=" O3G ANP B 701 " pdb="MG MG B 702 " model vdw 2.095 2.170 nonbonded pdb=" OE1 GLN B 517 " pdb="MG MG B 702 " model vdw 2.117 2.170 ... (remaining 74255 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 'B' } 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=0.00 max=1.00 mean=0.95 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: 1.340 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: 7.210 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.480 Find NCS groups from input model: 0.540 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 0.224 9568 Z= 0.475 Angle : 1.044 14.289 12942 Z= 0.511 Chirality : 0.052 0.272 1494 Planarity : 0.006 0.045 1616 Dihedral : 17.189 131.107 3606 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % 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: -3.29 (0.20), residues: 1166 helix: -1.52 (0.14), residues: 788 sheet: -3.68 (0.43), residues: 82 loop : -3.03 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 100 HIS 0.005 0.001 HIS B 235 PHE 0.016 0.002 PHE A 179 TYR 0.011 0.002 TYR B 321 ARG 0.002 0.000 ARG B 534 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.040 Fit side-chains REVERT: A 202 ASP cc_start: 0.7765 (p0) cc_final: 0.7452 (p0) REVERT: A 284 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7570 (ttp80) REVERT: A 350 PHE cc_start: 0.7901 (t80) cc_final: 0.7439 (t80) REVERT: A 383 PHE cc_start: 0.8428 (t80) cc_final: 0.8197 (t80) REVERT: A 628 TYR cc_start: 0.8668 (m-80) cc_final: 0.8279 (m-10) REVERT: B 100 TRP cc_start: 0.7942 (t-100) cc_final: 0.7646 (t60) REVERT: B 202 ASP cc_start: 0.7785 (p0) cc_final: 0.7464 (p0) REVERT: B 284 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7575 (ttp80) REVERT: B 350 PHE cc_start: 0.7915 (t80) cc_final: 0.7448 (t80) REVERT: B 383 PHE cc_start: 0.8424 (t80) cc_final: 0.8182 (t80) REVERT: B 628 TYR cc_start: 0.8673 (m-80) cc_final: 0.8284 (m-10) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2631 time to fit residues: 63.3559 Evaluate side-chains 135 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 235 HIS A 347 ASN B 127 GLN B 235 HIS B 347 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9568 Z= 0.166 Angle : 0.509 6.885 12942 Z= 0.264 Chirality : 0.038 0.145 1494 Planarity : 0.003 0.031 1616 Dihedral : 12.872 153.228 1408 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.50 % Allowed : 15.47 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.24), residues: 1166 helix: 0.53 (0.18), residues: 788 sheet: -2.40 (0.62), residues: 48 loop : -2.87 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 463 HIS 0.002 0.000 HIS B 235 PHE 0.012 0.001 PHE B 195 TYR 0.007 0.001 TYR B 316 ARG 0.004 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 155 time to evaluate : 1.135 Fit side-chains REVERT: A 199 MET cc_start: 0.8625 (tpp) cc_final: 0.8220 (mpp) REVERT: A 202 ASP cc_start: 0.7775 (p0) cc_final: 0.7511 (p0) REVERT: A 284 ARG cc_start: 0.7789 (ttp80) cc_final: 0.7564 (ttp80) REVERT: A 350 PHE cc_start: 0.7941 (t80) cc_final: 0.7442 (t80) REVERT: A 383 PHE cc_start: 0.8367 (t80) cc_final: 0.8108 (t80) REVERT: A 396 TYR cc_start: 0.7313 (m-80) cc_final: 0.7106 (m-80) REVERT: A 616 ARG cc_start: 0.8197 (ttp-110) cc_final: 0.7983 (ttp80) REVERT: B 199 MET cc_start: 0.8582 (tpp) cc_final: 0.8164 (mpp) REVERT: B 202 ASP cc_start: 0.7793 (p0) cc_final: 0.7521 (p0) REVERT: B 284 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7633 (ttp80) REVERT: B 350 PHE cc_start: 0.7931 (t80) cc_final: 0.7416 (t80) REVERT: B 359 TYR cc_start: 0.8462 (t80) cc_final: 0.8197 (t80) REVERT: B 383 PHE cc_start: 0.8377 (t80) cc_final: 0.8142 (t80) REVERT: B 396 TYR cc_start: 0.7324 (m-80) cc_final: 0.7111 (m-80) REVERT: B 628 TYR cc_start: 0.8752 (m-80) cc_final: 0.8389 (m-10) outliers start: 15 outliers final: 10 residues processed: 163 average time/residue: 0.2235 time to fit residues: 49.7369 Evaluate side-chains 152 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 517 GLN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 9568 Z= 0.391 Angle : 0.624 6.828 12942 Z= 0.322 Chirality : 0.043 0.164 1494 Planarity : 0.004 0.032 1616 Dihedral : 10.719 141.429 1408 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.79 % Allowed : 18.56 % Favored : 78.64 % 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: -0.41 (0.25), residues: 1166 helix: 0.95 (0.18), residues: 782 sheet: -2.46 (0.63), residues: 48 loop : -2.90 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 463 HIS 0.004 0.001 HIS A 197 PHE 0.026 0.002 PHE B 234 TYR 0.011 0.002 TYR A 486 ARG 0.005 0.000 ARG B 616 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.094 Fit side-chains REVERT: A 199 MET cc_start: 0.8554 (tpp) cc_final: 0.8339 (mpp) REVERT: A 235 HIS cc_start: 0.7157 (m-70) cc_final: 0.5999 (m170) REVERT: A 284 ARG cc_start: 0.7867 (ttp80) cc_final: 0.7547 (tpp-160) REVERT: A 350 PHE cc_start: 0.8024 (t80) cc_final: 0.7519 (t80) REVERT: A 383 PHE cc_start: 0.8502 (t80) cc_final: 0.8218 (t80) REVERT: A 396 TYR cc_start: 0.7489 (m-80) cc_final: 0.6757 (m-10) REVERT: A 616 ARG cc_start: 0.8207 (ttp-110) cc_final: 0.7980 (ttp80) REVERT: A 628 TYR cc_start: 0.8864 (m-10) cc_final: 0.8582 (m-10) REVERT: B 199 MET cc_start: 0.8527 (tpp) cc_final: 0.8324 (mpp) REVERT: B 235 HIS cc_start: 0.7302 (m-70) cc_final: 0.6121 (m170) REVERT: B 284 ARG cc_start: 0.7861 (ttp80) cc_final: 0.7542 (tpp-160) REVERT: B 350 PHE cc_start: 0.8028 (t80) cc_final: 0.7516 (t80) REVERT: B 383 PHE cc_start: 0.8502 (t80) cc_final: 0.8230 (t80) REVERT: B 396 TYR cc_start: 0.7459 (m-80) cc_final: 0.6797 (m-10) outliers start: 28 outliers final: 23 residues processed: 163 average time/residue: 0.2257 time to fit residues: 50.7990 Evaluate side-chains 159 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9568 Z= 0.173 Angle : 0.484 6.608 12942 Z= 0.254 Chirality : 0.039 0.137 1494 Planarity : 0.003 0.032 1616 Dihedral : 10.259 143.655 1408 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.39 % Allowed : 18.96 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1166 helix: 1.53 (0.19), residues: 780 sheet: -2.27 (0.65), residues: 48 loop : -2.72 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 463 HIS 0.007 0.001 HIS A 235 PHE 0.015 0.001 PHE B 179 TYR 0.011 0.001 TYR A 269 ARG 0.004 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 TRP cc_start: 0.8378 (t-100) cc_final: 0.8164 (t-100) REVERT: A 235 HIS cc_start: 0.7239 (OUTLIER) cc_final: 0.6615 (m170) REVERT: A 284 ARG cc_start: 0.7824 (ttp80) cc_final: 0.7597 (ttp80) REVERT: A 347 ASN cc_start: 0.8228 (t0) cc_final: 0.8027 (t0) REVERT: A 350 PHE cc_start: 0.7952 (t80) cc_final: 0.7513 (t80) REVERT: A 383 PHE cc_start: 0.8383 (t80) cc_final: 0.8123 (t80) REVERT: A 616 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.8032 (ttp80) REVERT: B 232 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7731 (mmp) REVERT: B 235 HIS cc_start: 0.7245 (OUTLIER) cc_final: 0.6661 (m170) REVERT: B 284 ARG cc_start: 0.7807 (ttp80) cc_final: 0.7593 (ttp80) REVERT: B 347 ASN cc_start: 0.8233 (t0) cc_final: 0.8027 (t0) REVERT: B 350 PHE cc_start: 0.7955 (t80) cc_final: 0.7532 (t80) REVERT: B 383 PHE cc_start: 0.8386 (t80) cc_final: 0.8141 (t80) REVERT: B 392 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7773 (tp) outliers start: 34 outliers final: 22 residues processed: 170 average time/residue: 0.2282 time to fit residues: 53.1345 Evaluate side-chains 164 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 538 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 0.0070 chunk 1 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9568 Z= 0.256 Angle : 0.534 6.630 12942 Z= 0.278 Chirality : 0.040 0.140 1494 Planarity : 0.003 0.031 1616 Dihedral : 9.945 132.820 1408 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.09 % Allowed : 19.86 % 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: 0.43 (0.25), residues: 1166 helix: 1.64 (0.19), residues: 776 sheet: -2.21 (0.65), residues: 48 loop : -2.64 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 463 HIS 0.006 0.001 HIS A 235 PHE 0.018 0.001 PHE A 234 TYR 0.018 0.001 TYR A 628 ARG 0.006 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 140 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 TRP cc_start: 0.8427 (t-100) cc_final: 0.8223 (t-100) REVERT: A 199 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8116 (mpp) REVERT: A 235 HIS cc_start: 0.7203 (OUTLIER) cc_final: 0.6549 (m170) REVERT: A 284 ARG cc_start: 0.7826 (ttp80) cc_final: 0.7485 (tpp-160) REVERT: A 347 ASN cc_start: 0.8332 (t0) cc_final: 0.8051 (t0) REVERT: A 350 PHE cc_start: 0.7956 (t80) cc_final: 0.7495 (t80) REVERT: A 383 PHE cc_start: 0.8419 (t80) cc_final: 0.8184 (t80) REVERT: A 616 ARG cc_start: 0.8209 (ttp-110) cc_final: 0.7992 (ttp80) REVERT: A 628 TYR cc_start: 0.8842 (m-10) cc_final: 0.8634 (m-80) REVERT: B 199 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8046 (mpp) REVERT: B 232 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7651 (mmp) REVERT: B 235 HIS cc_start: 0.7284 (OUTLIER) cc_final: 0.6701 (m170) REVERT: B 284 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7609 (ttp80) REVERT: B 347 ASN cc_start: 0.8333 (t0) cc_final: 0.8046 (t0) REVERT: B 350 PHE cc_start: 0.8009 (t80) cc_final: 0.7546 (t80) REVERT: B 383 PHE cc_start: 0.8420 (t80) cc_final: 0.8164 (t80) REVERT: B 392 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7806 (tp) REVERT: B 628 TYR cc_start: 0.8842 (m-80) cc_final: 0.8594 (m-10) outliers start: 41 outliers final: 30 residues processed: 165 average time/residue: 0.2292 time to fit residues: 51.9946 Evaluate side-chains 172 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9568 Z= 0.256 Angle : 0.533 6.621 12942 Z= 0.276 Chirality : 0.041 0.139 1494 Planarity : 0.003 0.031 1616 Dihedral : 9.537 125.146 1408 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.29 % Allowed : 20.26 % Favored : 75.45 % 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: 0.57 (0.25), residues: 1166 helix: 1.73 (0.19), residues: 776 sheet: -2.17 (0.65), residues: 48 loop : -2.53 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 463 HIS 0.006 0.001 HIS B 235 PHE 0.018 0.001 PHE B 234 TYR 0.011 0.001 TYR A 628 ARG 0.006 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 199 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8068 (mpp) REVERT: A 235 HIS cc_start: 0.7171 (OUTLIER) cc_final: 0.6560 (m170) REVERT: A 284 ARG cc_start: 0.7812 (ttp80) cc_final: 0.7477 (tpp-160) REVERT: A 347 ASN cc_start: 0.8343 (t0) cc_final: 0.8004 (t0) REVERT: A 350 PHE cc_start: 0.8002 (t80) cc_final: 0.7481 (t80) REVERT: A 383 PHE cc_start: 0.8409 (t80) cc_final: 0.8149 (t80) REVERT: A 616 ARG cc_start: 0.8211 (ttp-110) cc_final: 0.7989 (ttp80) REVERT: A 628 TYR cc_start: 0.8834 (m-10) cc_final: 0.8619 (m-80) REVERT: B 199 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8076 (mpp) REVERT: B 235 HIS cc_start: 0.7178 (OUTLIER) cc_final: 0.6049 (m170) REVERT: B 284 ARG cc_start: 0.7823 (ttp80) cc_final: 0.7597 (ttp80) REVERT: B 347 ASN cc_start: 0.8344 (t0) cc_final: 0.8002 (t0) REVERT: B 350 PHE cc_start: 0.8020 (t80) cc_final: 0.7532 (t80) REVERT: B 383 PHE cc_start: 0.8424 (t80) cc_final: 0.8204 (t80) REVERT: B 392 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7784 (tp) REVERT: B 396 TYR cc_start: 0.7555 (m-80) cc_final: 0.6906 (m-80) REVERT: B 628 TYR cc_start: 0.8850 (m-80) cc_final: 0.8624 (m-10) outliers start: 43 outliers final: 34 residues processed: 169 average time/residue: 0.2215 time to fit residues: 51.5257 Evaluate side-chains 177 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 138 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 0.0670 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9568 Z= 0.203 Angle : 0.500 6.581 12942 Z= 0.261 Chirality : 0.039 0.136 1494 Planarity : 0.003 0.031 1616 Dihedral : 9.049 119.429 1408 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.89 % Allowed : 20.56 % Favored : 75.55 % 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: 0.84 (0.25), residues: 1166 helix: 1.92 (0.19), residues: 776 sheet: -2.07 (0.65), residues: 48 loop : -2.37 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP B 463 HIS 0.006 0.001 HIS B 235 PHE 0.021 0.001 PHE A 234 TYR 0.010 0.001 TYR A 269 ARG 0.004 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 138 time to evaluate : 1.145 Fit side-chains REVERT: A 199 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8026 (mpp) REVERT: A 235 HIS cc_start: 0.7056 (OUTLIER) cc_final: 0.6049 (m170) REVERT: A 284 ARG cc_start: 0.7807 (ttp80) cc_final: 0.7581 (ttp80) REVERT: A 347 ASN cc_start: 0.8369 (t0) cc_final: 0.7969 (t0) REVERT: A 350 PHE cc_start: 0.8000 (t80) cc_final: 0.7492 (t80) REVERT: A 396 TYR cc_start: 0.7388 (m-80) cc_final: 0.6716 (m-80) REVERT: A 616 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7972 (ttp80) REVERT: B 199 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8029 (mpp) REVERT: B 232 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7721 (mmm) REVERT: B 235 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6010 (m170) REVERT: B 284 ARG cc_start: 0.7804 (ttp80) cc_final: 0.7577 (ttp80) REVERT: B 347 ASN cc_start: 0.8366 (t0) cc_final: 0.7963 (t0) REVERT: B 350 PHE cc_start: 0.7980 (t80) cc_final: 0.7480 (t80) REVERT: B 383 PHE cc_start: 0.8395 (t80) cc_final: 0.8194 (t80) REVERT: B 392 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7787 (tp) REVERT: B 396 TYR cc_start: 0.7415 (m-80) cc_final: 0.6797 (m-80) REVERT: B 628 TYR cc_start: 0.8848 (m-80) cc_final: 0.8618 (m-10) outliers start: 39 outliers final: 30 residues processed: 158 average time/residue: 0.2136 time to fit residues: 47.2461 Evaluate side-chains 173 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9568 Z= 0.206 Angle : 0.504 6.573 12942 Z= 0.263 Chirality : 0.039 0.140 1494 Planarity : 0.003 0.030 1616 Dihedral : 8.717 115.219 1408 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.49 % Allowed : 20.26 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1166 helix: 1.96 (0.19), residues: 776 sheet: -2.01 (0.65), residues: 48 loop : -2.27 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 463 HIS 0.006 0.001 HIS B 235 PHE 0.026 0.001 PHE A 383 TYR 0.010 0.001 TYR A 269 ARG 0.007 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 142 time to evaluate : 1.066 Fit side-chains REVERT: A 199 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8031 (mpp) REVERT: A 235 HIS cc_start: 0.7032 (OUTLIER) cc_final: 0.6140 (m170) REVERT: A 284 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7483 (tpp-160) REVERT: A 347 ASN cc_start: 0.8389 (t0) cc_final: 0.7958 (t0) REVERT: A 350 PHE cc_start: 0.7979 (t80) cc_final: 0.7473 (t80) REVERT: A 396 TYR cc_start: 0.7405 (m-80) cc_final: 0.6720 (m-80) REVERT: A 616 ARG cc_start: 0.8189 (ttp-110) cc_final: 0.7975 (ttp80) REVERT: B 199 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8022 (mpp) REVERT: B 232 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7695 (mmm) REVERT: B 235 HIS cc_start: 0.7046 (OUTLIER) cc_final: 0.6059 (m170) REVERT: B 284 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7446 (tpp-160) REVERT: B 347 ASN cc_start: 0.8390 (t0) cc_final: 0.7960 (t0) REVERT: B 350 PHE cc_start: 0.7973 (t80) cc_final: 0.7485 (t80) REVERT: B 392 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7791 (tp) REVERT: B 396 TYR cc_start: 0.7402 (m-80) cc_final: 0.6767 (m-80) REVERT: B 628 TYR cc_start: 0.8849 (m-80) cc_final: 0.8627 (m-10) outliers start: 45 outliers final: 33 residues processed: 166 average time/residue: 0.2236 time to fit residues: 51.0873 Evaluate side-chains 179 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 140 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9568 Z= 0.172 Angle : 0.490 6.555 12942 Z= 0.256 Chirality : 0.039 0.137 1494 Planarity : 0.003 0.029 1616 Dihedral : 8.274 107.006 1408 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.79 % Allowed : 21.36 % Favored : 74.85 % 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: 1.16 (0.26), residues: 1166 helix: 2.08 (0.19), residues: 780 sheet: -1.91 (0.66), residues: 48 loop : -2.08 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 463 HIS 0.006 0.001 HIS B 235 PHE 0.020 0.001 PHE A 234 TYR 0.010 0.001 TYR A 269 ARG 0.007 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 1.065 Fit side-chains REVERT: A 199 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8032 (mpp) REVERT: A 235 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6162 (m170) REVERT: A 284 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7576 (ttp80) REVERT: A 347 ASN cc_start: 0.8392 (t0) cc_final: 0.8004 (t0) REVERT: A 396 TYR cc_start: 0.7397 (m-80) cc_final: 0.6769 (m-80) REVERT: A 616 ARG cc_start: 0.8181 (ttp-110) cc_final: 0.7974 (ttp80) REVERT: B 199 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8149 (mpp) REVERT: B 232 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7677 (mmm) REVERT: B 235 HIS cc_start: 0.7005 (OUTLIER) cc_final: 0.6103 (m170) REVERT: B 284 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7610 (ttp80) REVERT: B 347 ASN cc_start: 0.8393 (t0) cc_final: 0.7991 (t0) REVERT: B 350 PHE cc_start: 0.7959 (t80) cc_final: 0.7471 (t80) REVERT: B 392 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7833 (tp) REVERT: B 396 TYR cc_start: 0.7389 (m-80) cc_final: 0.6804 (m-80) outliers start: 38 outliers final: 31 residues processed: 170 average time/residue: 0.2180 time to fit residues: 51.0031 Evaluate side-chains 175 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 138 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 586 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9568 Z= 0.201 Angle : 0.517 7.716 12942 Z= 0.271 Chirality : 0.040 0.168 1494 Planarity : 0.003 0.033 1616 Dihedral : 8.163 105.424 1408 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.89 % Allowed : 21.16 % Favored : 74.95 % 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: 1.18 (0.26), residues: 1166 helix: 2.11 (0.19), residues: 776 sheet: -1.87 (0.67), residues: 48 loop : -2.09 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 463 HIS 0.006 0.001 HIS B 235 PHE 0.020 0.001 PHE A 383 TYR 0.016 0.001 TYR B 628 ARG 0.007 0.000 ARG A 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 140 time to evaluate : 1.090 Fit side-chains REVERT: A 199 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8021 (mpp) REVERT: A 235 HIS cc_start: 0.7003 (OUTLIER) cc_final: 0.6166 (m170) REVERT: A 284 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7488 (tpp-160) REVERT: A 347 ASN cc_start: 0.8403 (t0) cc_final: 0.7928 (t0) REVERT: A 396 TYR cc_start: 0.7417 (m-80) cc_final: 0.6752 (m-80) REVERT: A 616 ARG cc_start: 0.8184 (ttp-110) cc_final: 0.7975 (ttp80) REVERT: B 199 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8035 (mpp) REVERT: B 232 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7691 (mmm) REVERT: B 235 HIS cc_start: 0.6997 (OUTLIER) cc_final: 0.6083 (m170) REVERT: B 284 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7453 (tpp-160) REVERT: B 347 ASN cc_start: 0.8421 (t0) cc_final: 0.7937 (t0) REVERT: B 350 PHE cc_start: 0.7966 (t80) cc_final: 0.7466 (t80) REVERT: B 392 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7841 (tp) REVERT: B 396 TYR cc_start: 0.7384 (m-80) cc_final: 0.6721 (m-80) outliers start: 39 outliers final: 32 residues processed: 161 average time/residue: 0.2293 time to fit residues: 50.8702 Evaluate side-chains 177 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 139 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.128372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105310 restraints weight = 12576.700| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.54 r_work: 0.3142 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9568 Z= 0.227 Angle : 0.538 12.198 12942 Z= 0.277 Chirality : 0.040 0.157 1494 Planarity : 0.003 0.031 1616 Dihedral : 8.113 104.729 1408 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.99 % Allowed : 21.16 % Favored : 74.85 % 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: 1.13 (0.25), residues: 1166 helix: 2.06 (0.19), residues: 776 sheet: -1.87 (0.67), residues: 48 loop : -2.06 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 463 HIS 0.006 0.001 HIS A 235 PHE 0.017 0.001 PHE A 383 TYR 0.012 0.001 TYR B 628 ARG 0.007 0.000 ARG B 424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2002.49 seconds wall clock time: 36 minutes 42.86 seconds (2202.86 seconds total)