Starting phenix.real_space_refine on Tue Feb 3 18:32:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9h_65777/02_2026/9w9h_65777_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9h_65777/02_2026/9w9h_65777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w9h_65777/02_2026/9w9h_65777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9h_65777/02_2026/9w9h_65777.map" model { file = "/net/cci-nas-00/data/ceres_data/9w9h_65777/02_2026/9w9h_65777_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9h_65777/02_2026/9w9h_65777_neut.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 3888 2.51 5 N 1020 2.21 5 O 1130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6085 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 668 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 74} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 869 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "C" Number of atoms: 4548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4548 Classifications: {'peptide': 561} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 548} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.01, per 1000 atoms: 0.17 Number of scatterers: 6085 At special positions: 0 Unit cell: (74.801, 90.789, 139.324, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1130 8.00 N 1020 7.00 C 3888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 351.8 milliseconds 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1446 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 2 sheets defined 73.9% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 580 through 598 Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 623 through 626 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 650 through 654 Processing helix chain 'B' and resid 575 through 590 Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 640 through 650 removed outlier: 3.682A pdb=" N ILE B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 656 removed outlier: 3.925A pdb=" N TYR B 655 " --> pdb=" O GLU B 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 removed outlier: 3.851A pdb=" N TYR C 143 " --> pdb=" O GLU C 140 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU C 144 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 161 removed outlier: 3.586A pdb=" N LEU C 159 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 172 Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.984A pdb=" N GLU C 185 " --> pdb=" O ARG C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 196 Processing helix chain 'C' and resid 200 through 206 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 210 through 217 Processing helix chain 'C' and resid 218 through 244 removed outlier: 3.538A pdb=" N LEU C 222 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 290 removed outlier: 4.550A pdb=" N LYS C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 301 Processing helix chain 'C' and resid 303 through 312 removed outlier: 3.752A pdb=" N MET C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 331 Processing helix chain 'C' and resid 333 through 343 Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 357 through 372 removed outlier: 3.551A pdb=" N LEU C 361 " --> pdb=" O HIS C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 384 removed outlier: 3.609A pdb=" N VAL C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 393 removed outlier: 4.437A pdb=" N LYS C 389 " --> pdb=" O GLY C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 412 Processing helix chain 'C' and resid 413 through 421 removed outlier: 4.222A pdb=" N SER C 418 " --> pdb=" O ARG C 415 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET C 419 " --> pdb=" O PHE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 436 Processing helix chain 'C' and resid 442 through 453 Processing helix chain 'C' and resid 455 through 463 removed outlier: 3.504A pdb=" N LEU C 461 " --> pdb=" O ARG C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 478 Processing helix chain 'C' and resid 480 through 492 Processing helix chain 'C' and resid 495 through 500 removed outlier: 3.871A pdb=" N ASN C 499 " --> pdb=" O GLY C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 503 No H-bonds generated for 'chain 'C' and resid 501 through 503' Processing helix chain 'C' and resid 504 through 513 removed outlier: 3.673A pdb=" N GLN C 511 " --> pdb=" O ASP C 507 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER C 513 " --> pdb=" O ALA C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 530 removed outlier: 3.863A pdb=" N GLU C 523 " --> pdb=" O GLU C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 545 removed outlier: 4.282A pdb=" N VAL C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 554 removed outlier: 4.492A pdb=" N PHE C 550 " --> pdb=" O LYS C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 576 Processing helix chain 'C' and resid 581 through 589 removed outlier: 4.200A pdb=" N GLY C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 601 removed outlier: 3.646A pdb=" N ALA C 593 " --> pdb=" O GLY C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 620 removed outlier: 4.653A pdb=" N PHE C 620 " --> pdb=" O TYR C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 630 removed outlier: 3.871A pdb=" N VAL C 627 " --> pdb=" O ALA C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 641 Processing helix chain 'C' and resid 646 through 664 removed outlier: 3.767A pdb=" N ILE C 659 " --> pdb=" O ASN C 655 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU C 662 " --> pdb=" O ASP C 658 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR C 663 " --> pdb=" O ILE C 659 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP C 664 " --> pdb=" O ILE C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 680 removed outlier: 3.527A pdb=" N ALA C 668 " --> pdb=" O ASP C 664 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS C 675 " --> pdb=" O ILE C 671 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N TRP C 678 " --> pdb=" O GLU C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 686 Processing sheet with id=AA1, first strand: chain 'A' and resid 610 through 613 Processing sheet with id=AA2, first strand: chain 'B' and resid 604 through 606 335 hydrogen bonds defined for protein. 963 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: 0.75 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1996 1.34 - 1.46: 992 1.46 - 1.58: 3122 1.58 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 6191 Sorted by residual: bond pdb=" N ASP C 136 " pdb=" CA ASP C 136 " ideal model delta sigma weight residual 1.454 1.491 -0.036 1.16e-02 7.43e+03 9.83e+00 bond pdb=" N VAL C 191 " pdb=" CA VAL C 191 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.81e+00 bond pdb=" N ILE C 426 " pdb=" CA ILE C 426 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.58e+00 bond pdb=" N VAL A 637 " pdb=" CA VAL A 637 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.36e+00 bond pdb=" N GLU A 642 " pdb=" CA GLU A 642 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.22e-02 6.72e+03 8.12e+00 ... (remaining 6186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 8163 2.48 - 4.97: 168 4.97 - 7.45: 14 7.45 - 9.93: 5 9.93 - 12.41: 1 Bond angle restraints: 8351 Sorted by residual: angle pdb=" N ILE C 200 " pdb=" CA ILE C 200 " pdb=" C ILE C 200 " ideal model delta sigma weight residual 111.48 106.40 5.08 9.40e-01 1.13e+00 2.92e+01 angle pdb=" C LEU C 547 " pdb=" N VAL C 548 " pdb=" CA VAL C 548 " ideal model delta sigma weight residual 122.13 113.92 8.21 1.85e+00 2.92e-01 1.97e+01 angle pdb=" CB MET C 571 " pdb=" CG MET C 571 " pdb=" SD MET C 571 " ideal model delta sigma weight residual 112.70 125.11 -12.41 3.00e+00 1.11e-01 1.71e+01 angle pdb=" C ASP C 424 " pdb=" CA ASP C 424 " pdb=" CB ASP C 424 " ideal model delta sigma weight residual 109.80 114.85 -5.05 1.23e+00 6.61e-01 1.69e+01 angle pdb=" CA LYS C 543 " pdb=" C LYS C 543 " pdb=" O LYS C 543 " ideal model delta sigma weight residual 120.82 116.84 3.98 1.05e+00 9.07e-01 1.43e+01 ... (remaining 8346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 3197 17.23 - 34.47: 464 34.47 - 51.70: 139 51.70 - 68.93: 25 68.93 - 86.17: 10 Dihedral angle restraints: 3835 sinusoidal: 1626 harmonic: 2209 Sorted by residual: dihedral pdb=" CA LYS C 675 " pdb=" C LYS C 675 " pdb=" N PHE C 676 " pdb=" CA PHE C 676 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA THR C 195 " pdb=" C THR C 195 " pdb=" N ASN C 196 " pdb=" CA ASN C 196 " ideal model delta harmonic sigma weight residual 180.00 158.67 21.33 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA PHE C 201 " pdb=" C PHE C 201 " pdb=" N PHE C 202 " pdb=" CA PHE C 202 " ideal model delta harmonic sigma weight residual 180.00 162.19 17.81 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 3832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 753 0.054 - 0.109: 168 0.109 - 0.163: 20 0.163 - 0.218: 4 0.218 - 0.272: 2 Chirality restraints: 947 Sorted by residual: chirality pdb=" CB ILE C 639 " pdb=" CA ILE C 639 " pdb=" CG1 ILE C 639 " pdb=" CG2 ILE C 639 " 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 C 146 " pdb=" CA ILE C 146 " pdb=" CG1 ILE C 146 " pdb=" CG2 ILE C 146 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA GLN C 189 " pdb=" N GLN C 189 " pdb=" C GLN C 189 " pdb=" CB GLN C 189 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 944 not shown) Planarity restraints: 1065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 675 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C LYS C 675 " 0.055 2.00e-02 2.50e+03 pdb=" O LYS C 675 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE C 676 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 543 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C LYS C 543 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS C 543 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU C 544 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 278 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C LEU C 278 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU C 278 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU C 279 " -0.013 2.00e-02 2.50e+03 ... (remaining 1062 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 3 2.41 - 3.03: 3711 3.03 - 3.65: 9246 3.65 - 4.28: 13988 4.28 - 4.90: 22459 Nonbonded interactions: 49407 Sorted by model distance: nonbonded pdb=" O ASN C 131 " pdb=" ND2 ASN C 131 " model vdw 1.786 3.120 nonbonded pdb=" CE3 TRP A 612 " pdb=" OE2 GLU A 614 " model vdw 2.198 3.340 nonbonded pdb=" CZ3 TRP A 612 " pdb=" OE2 GLU A 614 " model vdw 2.321 3.340 nonbonded pdb=" O TYR C 422 " pdb=" OG1 THR C 423 " model vdw 2.504 3.040 nonbonded pdb=" CG2 ILE C 198 " pdb=" CG2 VAL C 281 " model vdw 2.516 3.880 ... (remaining 49402 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.010 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:9.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 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 : 0.006 0.041 6191 Z= 0.298 Angle : 0.840 12.415 8351 Z= 0.478 Chirality : 0.047 0.272 947 Planarity : 0.005 0.037 1065 Dihedral : 18.013 86.168 2389 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.49 % Allowed : 26.98 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.31), residues: 736 helix: -0.04 (0.24), residues: 508 sheet: None (None), residues: 0 loop : -2.08 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 300 TYR 0.015 0.002 TYR C 138 PHE 0.012 0.002 PHE C 620 TRP 0.010 0.002 TRP A 612 HIS 0.005 0.002 HIS B 584 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 6191) covalent geometry : angle 0.84015 ( 8351) hydrogen bonds : bond 0.16245 ( 335) hydrogen bonds : angle 6.48308 ( 963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 135 MET cc_start: 0.4326 (tpp) cc_final: 0.4119 (tpp) REVERT: C 265 PHE cc_start: 0.7091 (t80) cc_final: 0.6628 (t80) REVERT: C 302 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7750 (mtpt) REVERT: C 347 GLU cc_start: 0.7364 (mp0) cc_final: 0.7036 (mp0) REVERT: C 488 ARG cc_start: 0.7858 (ttt180) cc_final: 0.7585 (ttt180) REVERT: C 511 GLN cc_start: 0.6721 (mm-40) cc_final: 0.6152 (mm-40) REVERT: C 578 ASP cc_start: 0.8186 (t0) cc_final: 0.7211 (t0) outliers start: 17 outliers final: 6 residues processed: 185 average time/residue: 0.4451 time to fit residues: 86.4206 Evaluate side-chains 166 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 284 TYR Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 670 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 ASN C 255 GLN C 383 GLN C 409 HIS C 493 HIS ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.193347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.156824 restraints weight = 9058.993| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.31 r_work: 0.3891 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6191 Z= 0.159 Angle : 0.669 9.967 8351 Z= 0.336 Chirality : 0.042 0.208 947 Planarity : 0.004 0.044 1065 Dihedral : 6.273 56.990 813 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.67 % Favored : 96.20 % Rotamer: Outliers : 5.13 % Allowed : 25.95 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.31), residues: 736 helix: 0.38 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.68 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 300 TYR 0.008 0.001 TYR C 616 PHE 0.016 0.002 PHE C 615 TRP 0.013 0.001 TRP A 612 HIS 0.008 0.002 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6191) covalent geometry : angle 0.66924 ( 8351) hydrogen bonds : bond 0.05016 ( 335) hydrogen bonds : angle 4.79347 ( 963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 135 MET cc_start: 0.5532 (tpp) cc_final: 0.4846 (tpp) REVERT: C 149 LYS cc_start: 0.8736 (mmtm) cc_final: 0.7972 (mmmt) REVERT: C 169 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7991 (tt) REVERT: C 204 PHE cc_start: 0.8513 (m-80) cc_final: 0.8291 (m-80) REVERT: C 225 ASN cc_start: 0.8044 (m-40) cc_final: 0.7843 (m-40) REVERT: C 261 TYR cc_start: 0.7690 (t80) cc_final: 0.7203 (t80) REVERT: C 265 PHE cc_start: 0.7153 (t80) cc_final: 0.6800 (t80) REVERT: C 347 GLU cc_start: 0.7386 (mp0) cc_final: 0.7126 (mp0) REVERT: C 404 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7451 (mmt) REVERT: C 511 GLN cc_start: 0.6951 (mm-40) cc_final: 0.6272 (mm-40) REVERT: C 523 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7055 (mm-30) REVERT: C 567 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6963 (mm-30) REVERT: C 578 ASP cc_start: 0.8353 (t0) cc_final: 0.7646 (t0) REVERT: C 601 GLN cc_start: 0.7488 (mm-40) cc_final: 0.7242 (mm-40) REVERT: C 608 VAL cc_start: 0.7812 (m) cc_final: 0.7495 (t) outliers start: 35 outliers final: 11 residues processed: 187 average time/residue: 0.4269 time to fit residues: 83.7751 Evaluate side-chains 178 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 284 TYR Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 503 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 29 optimal weight: 20.0000 chunk 15 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 50.0000 chunk 32 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 GLN ** C 655 ASN ** 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 = 0.4456 r_free = 0.4456 target = 0.191945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.154430 restraints weight = 8780.648| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.31 r_work: 0.3852 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6191 Z= 0.186 Angle : 0.651 7.586 8351 Z= 0.331 Chirality : 0.043 0.218 947 Planarity : 0.004 0.043 1065 Dihedral : 5.780 53.202 807 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.08 % Favored : 95.79 % Rotamer: Outliers : 5.87 % Allowed : 26.25 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.31), residues: 736 helix: 0.54 (0.23), residues: 511 sheet: None (None), residues: 0 loop : -1.61 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 378 TYR 0.011 0.001 TYR C 408 PHE 0.016 0.002 PHE C 620 TRP 0.009 0.001 TRP C 538 HIS 0.012 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 6191) covalent geometry : angle 0.65074 ( 8351) hydrogen bonds : bond 0.05238 ( 335) hydrogen bonds : angle 4.71191 ( 963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 135 MET cc_start: 0.5768 (tpp) cc_final: 0.5072 (tpp) REVERT: C 161 ARG cc_start: 0.7241 (ttm-80) cc_final: 0.7002 (ttm-80) REVERT: C 169 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8083 (tt) REVERT: C 184 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7164 (mtm110) REVERT: C 204 PHE cc_start: 0.8571 (m-80) cc_final: 0.8350 (m-80) REVERT: C 261 TYR cc_start: 0.7738 (t80) cc_final: 0.7225 (t80) REVERT: C 265 PHE cc_start: 0.7204 (t80) cc_final: 0.6792 (t80) REVERT: C 310 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8222 (ttmt) REVERT: C 334 MET cc_start: 0.6447 (tpt) cc_final: 0.6247 (tpt) REVERT: C 347 GLU cc_start: 0.7373 (mp0) cc_final: 0.7112 (mp0) REVERT: C 356 GLU cc_start: 0.7105 (pm20) cc_final: 0.6870 (pm20) REVERT: C 380 LYS cc_start: 0.8444 (mmmm) cc_final: 0.8129 (mmmm) REVERT: C 404 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7422 (mmt) REVERT: C 511 GLN cc_start: 0.6964 (mm-40) cc_final: 0.6228 (mm-40) REVERT: C 578 ASP cc_start: 0.8412 (t0) cc_final: 0.7725 (t0) REVERT: C 601 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7273 (mm-40) REVERT: C 618 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.6970 (mtm) REVERT: C 665 GLU cc_start: 0.6871 (pm20) cc_final: 0.6637 (pm20) outliers start: 40 outliers final: 18 residues processed: 186 average time/residue: 0.4579 time to fit residues: 88.8976 Evaluate side-chains 188 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 284 TYR Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 503 ASP Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 641 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 30.0000 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 ASN C 225 ASN ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.191894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.154068 restraints weight = 8843.428| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.32 r_work: 0.3847 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6191 Z= 0.183 Angle : 0.649 8.399 8351 Z= 0.330 Chirality : 0.043 0.208 947 Planarity : 0.004 0.065 1065 Dihedral : 5.825 56.629 807 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.92 % Rotamer: Outliers : 6.16 % Allowed : 27.13 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.31), residues: 736 helix: 0.43 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.95 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 378 TYR 0.014 0.001 TYR C 545 PHE 0.016 0.002 PHE C 620 TRP 0.008 0.001 TRP C 538 HIS 0.012 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 6191) covalent geometry : angle 0.64908 ( 8351) hydrogen bonds : bond 0.05088 ( 335) hydrogen bonds : angle 4.65614 ( 963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: C 135 MET cc_start: 0.5922 (tpp) cc_final: 0.5259 (tpp) REVERT: C 161 ARG cc_start: 0.7317 (ttm-80) cc_final: 0.7087 (ttm-80) REVERT: C 169 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8112 (tt) REVERT: C 204 PHE cc_start: 0.8562 (m-80) cc_final: 0.8298 (m-80) REVERT: C 225 ASN cc_start: 0.8067 (m110) cc_final: 0.7706 (m110) REVERT: C 261 TYR cc_start: 0.7697 (t80) cc_final: 0.7204 (t80) REVERT: C 265 PHE cc_start: 0.7226 (t80) cc_final: 0.6284 (t80) REVERT: C 269 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.6730 (mp10) REVERT: C 310 LYS cc_start: 0.8475 (ttmt) cc_final: 0.8250 (ttmt) REVERT: C 316 ASN cc_start: 0.7815 (t0) cc_final: 0.7577 (t0) REVERT: C 334 MET cc_start: 0.6373 (tpt) cc_final: 0.6170 (tpt) REVERT: C 347 GLU cc_start: 0.7359 (mp0) cc_final: 0.7100 (mp0) REVERT: C 356 GLU cc_start: 0.7145 (pm20) cc_final: 0.6902 (pm20) REVERT: C 380 LYS cc_start: 0.8416 (mmmm) cc_final: 0.8072 (mmmm) REVERT: C 404 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7533 (mmm) REVERT: C 511 GLN cc_start: 0.6986 (mm-40) cc_final: 0.6238 (mm-40) REVERT: C 578 ASP cc_start: 0.8457 (t0) cc_final: 0.7878 (t0) REVERT: C 601 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7222 (mm-40) outliers start: 42 outliers final: 21 residues processed: 185 average time/residue: 0.4212 time to fit residues: 81.4888 Evaluate side-chains 188 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 TYR Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 503 ASP Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 641 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 39 optimal weight: 0.0670 chunk 35 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 66 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 0.0270 chunk 48 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 0.0020 overall best weight: 0.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 HIS ** C 655 ASN ** 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 = 0.4481 r_free = 0.4481 target = 0.194013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.156999 restraints weight = 8963.633| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.34 r_work: 0.3887 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6191 Z= 0.119 Angle : 0.599 8.553 8351 Z= 0.303 Chirality : 0.040 0.204 947 Planarity : 0.004 0.042 1065 Dihedral : 5.578 56.415 807 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.92 % Rotamer: Outliers : 5.87 % Allowed : 28.45 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.31), residues: 736 helix: 0.66 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -1.92 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 378 TYR 0.007 0.001 TYR C 545 PHE 0.011 0.001 PHE A 597 TRP 0.006 0.001 TRP C 667 HIS 0.012 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6191) covalent geometry : angle 0.59866 ( 8351) hydrogen bonds : bond 0.03950 ( 335) hydrogen bonds : angle 4.45628 ( 963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 MET cc_start: 0.6019 (tpp) cc_final: 0.5381 (tpp) REVERT: C 161 ARG cc_start: 0.7324 (ttm-80) cc_final: 0.7092 (ttm-80) REVERT: C 169 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8127 (tt) REVERT: C 204 PHE cc_start: 0.8506 (m-80) cc_final: 0.8197 (m-80) REVERT: C 261 TYR cc_start: 0.7658 (t80) cc_final: 0.7161 (t80) REVERT: C 265 PHE cc_start: 0.7125 (t80) cc_final: 0.6726 (t80) REVERT: C 302 LYS cc_start: 0.8033 (mtpt) cc_final: 0.7788 (mtpt) REVERT: C 310 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8226 (ttmt) REVERT: C 343 MET cc_start: 0.7437 (tpp) cc_final: 0.7185 (tpt) REVERT: C 347 GLU cc_start: 0.7264 (mp0) cc_final: 0.7054 (mp0) REVERT: C 380 LYS cc_start: 0.8411 (mmmm) cc_final: 0.8087 (mmmm) REVERT: C 484 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7375 (mmm) REVERT: C 507 ASP cc_start: 0.8171 (m-30) cc_final: 0.7373 (m-30) REVERT: C 511 GLN cc_start: 0.6871 (mm-40) cc_final: 0.6139 (mm-40) REVERT: C 578 ASP cc_start: 0.8397 (t0) cc_final: 0.7642 (t0) REVERT: C 601 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7258 (mm-40) REVERT: C 618 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6568 (mtm) REVERT: C 663 TYR cc_start: 0.7784 (m-80) cc_final: 0.7569 (m-80) outliers start: 40 outliers final: 15 residues processed: 181 average time/residue: 0.3937 time to fit residues: 74.5986 Evaluate side-chains 177 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 641 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 25 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.0770 chunk 24 optimal weight: 0.0970 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 46 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 GLN C 428 GLN C 451 ASN C 493 HIS ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.193845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.156306 restraints weight = 8916.610| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.35 r_work: 0.3880 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6191 Z= 0.121 Angle : 0.599 8.362 8351 Z= 0.302 Chirality : 0.040 0.202 947 Planarity : 0.004 0.041 1065 Dihedral : 5.152 50.254 805 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.12 % Favored : 96.74 % Rotamer: Outliers : 5.57 % Allowed : 29.33 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.31), residues: 736 helix: 0.68 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.91 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 378 TYR 0.008 0.001 TYR C 408 PHE 0.013 0.001 PHE C 620 TRP 0.006 0.001 TRP C 538 HIS 0.011 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6191) covalent geometry : angle 0.59901 ( 8351) hydrogen bonds : bond 0.04050 ( 335) hydrogen bonds : angle 4.40996 ( 963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 589 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7187 (mt) REVERT: C 135 MET cc_start: 0.6165 (tpp) cc_final: 0.5536 (tpp) REVERT: C 149 LYS cc_start: 0.8856 (mmtm) cc_final: 0.8256 (mmtt) REVERT: C 161 ARG cc_start: 0.7368 (ttm-80) cc_final: 0.7133 (ttm-80) REVERT: C 169 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8178 (tt) REVERT: C 204 PHE cc_start: 0.8449 (m-80) cc_final: 0.8134 (m-80) REVERT: C 261 TYR cc_start: 0.7636 (t80) cc_final: 0.7110 (t80) REVERT: C 265 PHE cc_start: 0.7134 (t80) cc_final: 0.6208 (t80) REVERT: C 269 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7069 (mp10) REVERT: C 276 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6921 (tt0) REVERT: C 302 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7785 (mtpt) REVERT: C 310 LYS cc_start: 0.8447 (ttmt) cc_final: 0.8232 (ttmt) REVERT: C 343 MET cc_start: 0.7522 (tpp) cc_final: 0.7289 (tpt) REVERT: C 347 GLU cc_start: 0.7298 (mp0) cc_final: 0.7065 (mp0) REVERT: C 380 LYS cc_start: 0.8419 (mmmm) cc_final: 0.8121 (mmmm) REVERT: C 507 ASP cc_start: 0.8209 (m-30) cc_final: 0.7391 (m-30) REVERT: C 511 GLN cc_start: 0.6888 (mm-40) cc_final: 0.6336 (mm-40) REVERT: C 516 GLU cc_start: 0.6432 (mp0) cc_final: 0.6068 (mp0) REVERT: C 578 ASP cc_start: 0.8385 (t0) cc_final: 0.7693 (t0) REVERT: C 601 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7254 (mm-40) REVERT: C 618 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6689 (mtm) REVERT: C 663 TYR cc_start: 0.7804 (m-80) cc_final: 0.7585 (m-80) outliers start: 38 outliers final: 23 residues processed: 178 average time/residue: 0.4173 time to fit residues: 77.6815 Evaluate side-chains 185 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 503 ASP Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 659 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 chunk 56 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 ASN C 493 HIS ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.192311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.154462 restraints weight = 8860.296| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.36 r_work: 0.3852 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6191 Z= 0.147 Angle : 0.620 8.302 8351 Z= 0.313 Chirality : 0.041 0.201 947 Planarity : 0.004 0.042 1065 Dihedral : 5.144 47.022 805 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.67 % Favored : 96.20 % Rotamer: Outliers : 5.43 % Allowed : 31.09 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.31), residues: 736 helix: 0.70 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -1.89 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 378 TYR 0.011 0.001 TYR C 408 PHE 0.015 0.001 PHE C 620 TRP 0.006 0.001 TRP C 538 HIS 0.010 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6191) covalent geometry : angle 0.61964 ( 8351) hydrogen bonds : bond 0.04512 ( 335) hydrogen bonds : angle 4.46894 ( 963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.149 Fit side-chains REVERT: A 589 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7189 (mt) REVERT: C 135 MET cc_start: 0.6244 (tpp) cc_final: 0.5625 (tpp) REVERT: C 149 LYS cc_start: 0.8861 (mmtm) cc_final: 0.8259 (mmtt) REVERT: C 169 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8197 (tt) REVERT: C 204 PHE cc_start: 0.8501 (m-80) cc_final: 0.8200 (m-80) REVERT: C 225 ASN cc_start: 0.8005 (m110) cc_final: 0.7611 (m110) REVERT: C 261 TYR cc_start: 0.7645 (t80) cc_final: 0.7153 (t80) REVERT: C 265 PHE cc_start: 0.7161 (t80) cc_final: 0.6267 (t80) REVERT: C 269 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: C 299 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7515 (mtt) REVERT: C 316 ASN cc_start: 0.7852 (t160) cc_final: 0.7100 (t0) REVERT: C 347 GLU cc_start: 0.7362 (mp0) cc_final: 0.7106 (mp0) REVERT: C 356 GLU cc_start: 0.7131 (pm20) cc_final: 0.6866 (pm20) REVERT: C 460 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7679 (mp-120) REVERT: C 511 GLN cc_start: 0.6972 (mm-40) cc_final: 0.6374 (mm-40) REVERT: C 516 GLU cc_start: 0.6405 (mp0) cc_final: 0.5994 (mp0) REVERT: C 578 ASP cc_start: 0.8423 (t0) cc_final: 0.7693 (t0) REVERT: C 601 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7196 (mm-40) REVERT: C 618 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6884 (mtm) REVERT: C 663 TYR cc_start: 0.7863 (m-80) cc_final: 0.7640 (m-80) outliers start: 37 outliers final: 22 residues processed: 183 average time/residue: 0.4018 time to fit residues: 77.0660 Evaluate side-chains 190 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 TYR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 503 ASP Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 641 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 50 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 32 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 428 GLN C 451 ASN C 493 HIS ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.191904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.154706 restraints weight = 8919.498| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.28 r_work: 0.3865 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6191 Z= 0.155 Angle : 0.651 8.222 8351 Z= 0.324 Chirality : 0.042 0.203 947 Planarity : 0.004 0.042 1065 Dihedral : 4.917 41.718 803 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.67 % Favored : 96.20 % Rotamer: Outliers : 5.72 % Allowed : 30.50 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.31), residues: 736 helix: 0.58 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.94 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 378 TYR 0.010 0.001 TYR C 504 PHE 0.015 0.001 PHE C 620 TRP 0.007 0.001 TRP C 538 HIS 0.009 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6191) covalent geometry : angle 0.65105 ( 8351) hydrogen bonds : bond 0.04472 ( 335) hydrogen bonds : angle 4.53353 ( 963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 589 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7192 (mt) REVERT: C 135 MET cc_start: 0.6169 (tpp) cc_final: 0.5590 (tpp) REVERT: C 149 LYS cc_start: 0.8862 (mmtm) cc_final: 0.8296 (mmtt) REVERT: C 169 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8150 (tt) REVERT: C 204 PHE cc_start: 0.8469 (m-80) cc_final: 0.8185 (m-80) REVERT: C 225 ASN cc_start: 0.8043 (m110) cc_final: 0.7666 (m110) REVERT: C 261 TYR cc_start: 0.7594 (t80) cc_final: 0.7188 (t80) REVERT: C 265 PHE cc_start: 0.7141 (t80) cc_final: 0.6408 (t80) REVERT: C 269 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: C 299 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7547 (mtt) REVERT: C 347 GLU cc_start: 0.7304 (mp0) cc_final: 0.7082 (mp0) REVERT: C 460 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7676 (mp-120) REVERT: C 511 GLN cc_start: 0.6888 (mm-40) cc_final: 0.6316 (mm-40) REVERT: C 516 GLU cc_start: 0.6366 (mp0) cc_final: 0.5963 (mp0) REVERT: C 618 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6957 (mtm) REVERT: C 663 TYR cc_start: 0.7865 (m-80) cc_final: 0.7658 (m-80) outliers start: 39 outliers final: 23 residues processed: 183 average time/residue: 0.4340 time to fit residues: 83.2952 Evaluate side-chains 187 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 TYR Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 400 LYS Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 641 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 44 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 451 ASN C 655 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.191103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.153482 restraints weight = 9025.080| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.32 r_work: 0.3851 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6191 Z= 0.171 Angle : 0.661 8.218 8351 Z= 0.332 Chirality : 0.043 0.204 947 Planarity : 0.004 0.042 1065 Dihedral : 4.997 41.532 803 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.08 % Favored : 95.79 % Rotamer: Outliers : 5.72 % Allowed : 30.79 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.31), residues: 736 helix: 0.47 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.87 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 378 TYR 0.012 0.001 TYR C 504 PHE 0.016 0.002 PHE C 620 TRP 0.010 0.001 TRP C 538 HIS 0.011 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 6191) covalent geometry : angle 0.66106 ( 8351) hydrogen bonds : bond 0.04791 ( 335) hydrogen bonds : angle 4.60721 ( 963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 589 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7209 (mt) REVERT: C 135 MET cc_start: 0.6271 (tpp) cc_final: 0.5676 (tpp) REVERT: C 149 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8301 (mmtt) REVERT: C 169 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8185 (tt) REVERT: C 225 ASN cc_start: 0.8066 (m110) cc_final: 0.7657 (m110) REVERT: C 261 TYR cc_start: 0.7638 (t80) cc_final: 0.7214 (t80) REVERT: C 265 PHE cc_start: 0.7199 (t80) cc_final: 0.6468 (t80) REVERT: C 269 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: C 299 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7544 (mtt) REVERT: C 347 GLU cc_start: 0.7345 (mp0) cc_final: 0.7133 (mp0) REVERT: C 460 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7720 (mp-120) REVERT: C 479 LYS cc_start: 0.6676 (mmtt) cc_final: 0.6328 (mttp) REVERT: C 488 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7867 (ttt180) REVERT: C 618 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7107 (mtm) REVERT: C 663 TYR cc_start: 0.7913 (m-80) cc_final: 0.7702 (m-80) outliers start: 39 outliers final: 24 residues processed: 180 average time/residue: 0.4632 time to fit residues: 87.3432 Evaluate side-chains 195 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 TYR Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 400 LYS Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 641 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 58 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 62 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 451 ASN C 493 HIS C 655 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.191988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.154506 restraints weight = 8871.482| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.31 r_work: 0.3861 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6191 Z= 0.150 Angle : 0.665 8.193 8351 Z= 0.331 Chirality : 0.043 0.228 947 Planarity : 0.004 0.042 1065 Dihedral : 4.978 41.150 803 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.08 % Favored : 95.79 % Rotamer: Outliers : 5.13 % Allowed : 31.38 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.31), residues: 736 helix: 0.46 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.88 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 378 TYR 0.011 0.001 TYR C 545 PHE 0.015 0.001 PHE C 620 TRP 0.006 0.001 TRP C 538 HIS 0.006 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6191) covalent geometry : angle 0.66475 ( 8351) hydrogen bonds : bond 0.04485 ( 335) hydrogen bonds : angle 4.59576 ( 963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 589 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7207 (mt) REVERT: C 135 MET cc_start: 0.6243 (tpp) cc_final: 0.5660 (tpp) REVERT: C 149 LYS cc_start: 0.8880 (mmtm) cc_final: 0.8280 (mmtt) REVERT: C 169 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8193 (tt) REVERT: C 204 PHE cc_start: 0.8505 (m-80) cc_final: 0.8220 (m-80) REVERT: C 225 ASN cc_start: 0.8041 (m110) cc_final: 0.7673 (m110) REVERT: C 261 TYR cc_start: 0.7627 (t80) cc_final: 0.7195 (t80) REVERT: C 265 PHE cc_start: 0.7172 (t80) cc_final: 0.6433 (t80) REVERT: C 269 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7371 (mp10) REVERT: C 299 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7535 (mtt) REVERT: C 302 LYS cc_start: 0.8004 (mtpt) cc_final: 0.7745 (mtpt) REVERT: C 347 GLU cc_start: 0.7289 (mp0) cc_final: 0.7086 (mp0) REVERT: C 479 LYS cc_start: 0.6634 (mmtt) cc_final: 0.6286 (mttp) REVERT: C 488 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7860 (ttt180) REVERT: C 578 ASP cc_start: 0.8391 (t0) cc_final: 0.7778 (t0) REVERT: C 618 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7031 (mtm) REVERT: C 665 GLU cc_start: 0.7111 (pm20) cc_final: 0.6612 (pm20) REVERT: C 669 LYS cc_start: 0.7778 (ttmm) cc_final: 0.7566 (ttmm) outliers start: 35 outliers final: 21 residues processed: 180 average time/residue: 0.4612 time to fit residues: 86.9802 Evaluate side-chains 187 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 TYR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 400 LYS Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 628 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 0.0170 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 50.0000 chunk 67 optimal weight: 0.0770 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 ASN C 451 ASN C 655 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.192687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.155610 restraints weight = 8883.529| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.30 r_work: 0.3872 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6191 Z= 0.133 Angle : 0.653 8.557 8351 Z= 0.325 Chirality : 0.042 0.234 947 Planarity : 0.004 0.043 1065 Dihedral : 4.923 40.741 803 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.35 % Favored : 95.52 % Rotamer: Outliers : 4.84 % Allowed : 31.67 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.31), residues: 736 helix: 0.49 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.74 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 378 TYR 0.011 0.001 TYR C 545 PHE 0.014 0.001 PHE C 620 TRP 0.007 0.001 TRP C 538 HIS 0.005 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6191) covalent geometry : angle 0.65266 ( 8351) hydrogen bonds : bond 0.04154 ( 335) hydrogen bonds : angle 4.55893 ( 963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2412.13 seconds wall clock time: 41 minutes 39.10 seconds (2499.10 seconds total)