Starting phenix.real_space_refine on Tue Feb 11 14:12:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t6v_10387/02_2025/6t6v_10387.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t6v_10387/02_2025/6t6v_10387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t6v_10387/02_2025/6t6v_10387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t6v_10387/02_2025/6t6v_10387.map" model { file = "/net/cci-nas-00/data/ceres_data/6t6v_10387/02_2025/6t6v_10387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t6v_10387/02_2025/6t6v_10387.cif" } resolution = 4.5 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= 0.005 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 Ca 1 9.91 5 Fe 2 7.16 5 S 22 5.16 5 C 3881 2.51 5 N 977 2.21 5 O 985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5868 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5781 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 742, 5777 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 35, 'TRANS': 706} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 742, 5777 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 35, 'TRANS': 706} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 5963 Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {' CA': 1, 'HEM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY A 2 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 2 " occ=0.50 Time building chain proxies: 5.93, per 1000 atoms: 1.01 Number of scatterers: 5868 At special positions: 0 Unit cell: (79.268, 71.967, 105.343, 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) Fe 2 26.01 Ca 1 19.99 S 22 16.00 O 985 8.00 N 977 7.00 C 3881 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 1.5 seconds 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 2 sheets defined 69.4% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 removed outlier: 3.539A pdb=" N PHE A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 30 removed outlier: 3.799A pdb=" N VAL A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.533A pdb=" N LEU A 69 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 102 removed outlier: 3.817A pdb=" N LEU A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 127 Processing helix chain 'A' and resid 142 through 159 removed outlier: 3.921A pdb=" N ALA A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 171 removed outlier: 4.007A pdb=" N GLU A 171 " --> pdb=" O HIS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 199 Processing helix chain 'A' and resid 226 through 253 removed outlier: 3.679A pdb=" N VAL A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 309 Processing helix chain 'A' and resid 323 through 355 removed outlier: 3.551A pdb=" N PHE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Proline residue: A 352 - end of helix removed outlier: 3.785A pdb=" N ASN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 390 removed outlier: 3.745A pdb=" N GLY A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 435 Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 444 through 461 removed outlier: 4.277A pdb=" N LEU A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 473 through 485 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 514 through 529 removed outlier: 3.945A pdb=" N PHE A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 Processing helix chain 'A' and resid 545 through 555 removed outlier: 3.740A pdb=" N SER A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 560 removed outlier: 4.191A pdb=" N GLU A 559 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 556 through 560' Processing helix chain 'A' and resid 573 through 577 Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 586 through 601 removed outlier: 3.834A pdb=" N LEU A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 597 " --> pdb=" O PHE A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 611 removed outlier: 3.739A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 619 removed outlier: 4.280A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 Processing helix chain 'A' and resid 637 through 651 removed outlier: 4.090A pdb=" N LEU A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 670 Processing helix chain 'A' and resid 670 through 681 Processing helix chain 'A' and resid 682 through 697 removed outlier: 3.509A pdb=" N ILE A 686 " --> pdb=" O SER A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 703 removed outlier: 3.843A pdb=" N ARG A 703 " --> pdb=" O MET A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 709 Processing helix chain 'A' and resid 712 through 719 Processing helix chain 'A' and resid 720 through 742 removed outlier: 3.590A pdb=" N ASP A 724 " --> pdb=" O ARG A 720 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 removed outlier: 5.036A pdb=" N PHE A 49 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 removed outlier: 4.233A pdb=" N ILE A 72 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS A 75 " --> pdb=" O ILE A 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 334 hydrogen bonds defined for protein. 972 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 2618 1.40 - 1.57: 3403 1.57 - 1.75: 0 1.75 - 1.93: 44 1.93 - 2.10: 6 Bond restraints: 6071 Sorted by residual: bond pdb=" C3B HEM A 802 " pdb=" CAB HEM A 802 " ideal model delta sigma weight residual 1.544 1.473 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C3B HEM A 801 " pdb=" CAB HEM A 801 " ideal model delta sigma weight residual 1.544 1.474 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C3C HEM A 801 " pdb=" CAC HEM A 801 " ideal model delta sigma weight residual 1.544 1.474 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C3C HEM A 802 " pdb=" CAC HEM A 802 " ideal model delta sigma weight residual 1.544 1.474 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" CA LEU A 521 " pdb=" C LEU A 521 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.30e-02 5.92e+03 9.88e+00 ... (remaining 6066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 7568 2.10 - 4.19: 583 4.19 - 6.29: 125 6.29 - 8.39: 35 8.39 - 10.48: 15 Bond angle restraints: 8326 Sorted by residual: angle pdb=" C VAL A 560 " pdb=" N VAL A 561 " pdb=" CA VAL A 561 " ideal model delta sigma weight residual 120.24 125.28 -5.04 6.30e-01 2.52e+00 6.41e+01 angle pdb=" N GLN A 32 " pdb=" CA GLN A 32 " pdb=" C GLN A 32 " ideal model delta sigma weight residual 113.17 103.47 9.70 1.26e+00 6.30e-01 5.93e+01 angle pdb=" C VAL A 561 " pdb=" CA VAL A 561 " pdb=" CB VAL A 561 " ideal model delta sigma weight residual 114.35 107.17 7.18 1.06e+00 8.90e-01 4.59e+01 angle pdb=" N VAL A 561 " pdb=" CA VAL A 561 " pdb=" C VAL A 561 " ideal model delta sigma weight residual 112.61 122.40 -9.79 1.45e+00 4.76e-01 4.56e+01 angle pdb=" N GLY A 405 " pdb=" CA GLY A 405 " pdb=" C GLY A 405 " ideal model delta sigma weight residual 115.64 124.51 -8.87 1.46e+00 4.69e-01 3.69e+01 ... (remaining 8321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 2986 17.44 - 34.87: 282 34.87 - 52.31: 66 52.31 - 69.74: 14 69.74 - 87.18: 10 Dihedral angle restraints: 3358 sinusoidal: 1248 harmonic: 2110 Sorted by residual: dihedral pdb=" C2B HEM A 802 " pdb=" C3B HEM A 802 " pdb=" CAB HEM A 802 " pdb=" CBB HEM A 802 " ideal model delta sinusoidal sigma weight residual 180.00 99.38 80.62 2 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" C2C HEM A 801 " pdb=" C3C HEM A 801 " pdb=" CAC HEM A 801 " pdb=" CBC HEM A 801 " ideal model delta sinusoidal sigma weight residual 0.00 -61.73 61.73 2 1.00e+01 1.00e-02 3.72e+01 dihedral pdb=" C2B HEM A 801 " pdb=" C3B HEM A 801 " pdb=" CAB HEM A 801 " pdb=" CBB HEM A 801 " ideal model delta sinusoidal sigma weight residual 180.00 120.41 59.59 2 1.00e+01 1.00e-02 3.57e+01 ... (remaining 3355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 678 0.077 - 0.154: 156 0.154 - 0.231: 35 0.231 - 0.308: 9 0.308 - 0.386: 5 Chirality restraints: 883 Sorted by residual: chirality pdb=" CB THR A 546 " pdb=" CA THR A 546 " pdb=" OG1 THR A 546 " pdb=" CG2 THR A 546 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA THR A 578 " pdb=" N THR A 578 " pdb=" C THR A 578 " pdb=" CB THR A 578 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CB THR A 646 " pdb=" CA THR A 646 " pdb=" OG1 THR A 646 " pdb=" CG2 THR A 646 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 880 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 187 " -0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C ARG A 187 " 0.086 2.00e-02 2.50e+03 pdb=" O ARG A 187 " -0.032 2.00e-02 2.50e+03 pdb=" N GLN A 188 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 599 " -0.024 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C TRP A 599 " 0.082 2.00e-02 2.50e+03 pdb=" O TRP A 599 " -0.030 2.00e-02 2.50e+03 pdb=" N ASN A 600 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 286 " 0.023 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C LEU A 286 " -0.080 2.00e-02 2.50e+03 pdb=" O LEU A 286 " 0.030 2.00e-02 2.50e+03 pdb=" N PHE A 287 " 0.027 2.00e-02 2.50e+03 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 63 2.54 - 3.13: 4456 3.13 - 3.72: 10124 3.72 - 4.31: 12944 4.31 - 4.90: 20611 Nonbonded interactions: 48198 Sorted by model distance: nonbonded pdb=" O GLU A 28 " pdb=" CG GLN A 32 " model vdw 1.944 3.440 nonbonded pdb=" OE1 GLU A 407 " pdb="CA CA A 803 " model vdw 2.047 2.510 nonbonded pdb=" O GLU A 28 " pdb=" CB GLN A 32 " model vdw 2.090 3.440 nonbonded pdb=" NE2 HIS A 331 " pdb="FE HEM A 801 " model vdw 2.125 3.080 nonbonded pdb=" OH TYR A 408 " pdb=" O2A HEM A 802 " model vdw 2.161 3.040 ... (remaining 48193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.520 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.009 0.216 6071 Z= 0.594 Angle : 1.341 10.484 8326 Z= 0.759 Chirality : 0.076 0.386 883 Planarity : 0.009 0.051 1040 Dihedral : 15.460 87.178 2018 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Cbeta Deviations : 0.15 % 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: -4.09 (0.25), residues: 741 helix: -2.59 (0.17), residues: 488 sheet: None (None), residues: 0 loop : -2.60 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 338 HIS 0.020 0.003 HIS A 568 PHE 0.029 0.003 PHE A 493 TYR 0.026 0.003 TYR A 156 ARG 0.015 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9255 (m) cc_final: 0.8662 (m) REVERT: A 62 GLN cc_start: 0.9068 (mt0) cc_final: 0.8594 (mt0) REVERT: A 87 TRP cc_start: 0.8792 (t-100) cc_final: 0.7956 (t60) REVERT: A 88 LEU cc_start: 0.9579 (tp) cc_final: 0.9337 (tp) REVERT: A 93 MET cc_start: 0.8690 (mmt) cc_final: 0.8415 (mmp) REVERT: A 101 ARG cc_start: 0.9240 (tpp-160) cc_final: 0.8920 (mmm-85) REVERT: A 138 LYS cc_start: 0.9440 (mmtt) cc_final: 0.9083 (mmtm) REVERT: A 153 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6606 (tm-30) REVERT: A 157 ASP cc_start: 0.8098 (m-30) cc_final: 0.7395 (m-30) REVERT: A 296 GLN cc_start: 0.9452 (tm-30) cc_final: 0.9159 (tm-30) REVERT: A 404 GLN cc_start: 0.9337 (tt0) cc_final: 0.9090 (tt0) REVERT: A 420 PHE cc_start: 0.8903 (t80) cc_final: 0.8585 (t80) REVERT: A 424 CYS cc_start: 0.9549 (m) cc_final: 0.9310 (m) REVERT: A 468 TYR cc_start: 0.8719 (p90) cc_final: 0.8430 (p90) REVERT: A 477 MET cc_start: 0.8581 (tpp) cc_final: 0.8180 (tpp) REVERT: A 481 ARG cc_start: 0.9161 (ttt-90) cc_final: 0.8892 (ptm-80) REVERT: A 493 PHE cc_start: 0.9361 (m-10) cc_final: 0.9144 (m-80) REVERT: A 601 MET cc_start: 0.7937 (ttt) cc_final: 0.7262 (mmm) REVERT: A 621 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7007 (tm-30) REVERT: A 638 TYR cc_start: 0.9152 (m-80) cc_final: 0.8880 (m-10) REVERT: A 665 LYS cc_start: 0.8613 (pttp) cc_final: 0.8013 (pttm) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1685 time to fit residues: 44.8648 Evaluate side-chains 161 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 89 HIS A 217 HIS A 333 GLN ** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.097156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.070070 restraints weight = 35952.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074311 restraints weight = 17074.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077377 restraints weight = 10694.325| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6071 Z= 0.217 Angle : 0.846 21.740 8326 Z= 0.385 Chirality : 0.045 0.187 883 Planarity : 0.005 0.037 1040 Dihedral : 7.020 71.096 821 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: -2.37 (0.28), residues: 741 helix: -1.06 (0.21), residues: 497 sheet: None (None), residues: 0 loop : -2.45 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 480 HIS 0.008 0.002 HIS A 568 PHE 0.022 0.002 PHE A 727 TYR 0.020 0.002 TYR A 408 ARG 0.005 0.001 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9409 (mt0) cc_final: 0.9113 (mt0) REVERT: A 87 TRP cc_start: 0.9206 (t-100) cc_final: 0.8258 (t60) REVERT: A 93 MET cc_start: 0.8855 (mmt) cc_final: 0.8628 (mmp) REVERT: A 97 ASP cc_start: 0.9406 (t70) cc_final: 0.9194 (t0) REVERT: A 101 ARG cc_start: 0.9262 (tpp-160) cc_final: 0.8943 (mmm-85) REVERT: A 123 LEU cc_start: 0.9122 (mt) cc_final: 0.8869 (mt) REVERT: A 153 GLU cc_start: 0.7560 (tm-30) cc_final: 0.6637 (tm-30) REVERT: A 157 ASP cc_start: 0.7801 (m-30) cc_final: 0.6774 (m-30) REVERT: A 295 PHE cc_start: 0.9147 (t80) cc_final: 0.8926 (t80) REVERT: A 408 TYR cc_start: 0.9229 (m-80) cc_final: 0.8357 (m-80) REVERT: A 424 CYS cc_start: 0.9563 (m) cc_final: 0.9297 (m) REVERT: A 477 MET cc_start: 0.9035 (tpp) cc_final: 0.8529 (tpp) REVERT: A 481 ARG cc_start: 0.9081 (ttt-90) cc_final: 0.8623 (ttt-90) REVERT: A 505 PHE cc_start: 0.9334 (m-80) cc_final: 0.9053 (m-80) REVERT: A 515 MET cc_start: 0.8057 (mmt) cc_final: 0.7750 (mmp) REVERT: A 601 MET cc_start: 0.7672 (ttt) cc_final: 0.6922 (mmm) REVERT: A 621 GLN cc_start: 0.7306 (tm-30) cc_final: 0.7056 (tm-30) REVERT: A 683 LEU cc_start: 0.9537 (mm) cc_final: 0.9320 (mm) REVERT: A 708 MET cc_start: 0.8739 (mtm) cc_final: 0.8435 (mtm) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1447 time to fit residues: 38.8909 Evaluate side-chains 169 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 26 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN A 404 GLN A 672 ASN ** A 690 GLN ** 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 = 0.3515 r_free = 0.3515 target = 0.098380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.074270 restraints weight = 25079.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.077930 restraints weight = 13967.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.080621 restraints weight = 9324.650| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6071 Z= 0.217 Angle : 0.737 6.839 8326 Z= 0.360 Chirality : 0.044 0.182 883 Planarity : 0.005 0.033 1040 Dihedral : 6.972 67.668 821 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: -1.64 (0.30), residues: 741 helix: -0.47 (0.23), residues: 507 sheet: None (None), residues: 0 loop : -2.31 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 480 HIS 0.006 0.001 HIS A 568 PHE 0.021 0.001 PHE A 503 TYR 0.021 0.002 TYR A 638 ARG 0.007 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9539 (mt0) cc_final: 0.8889 (mt0) REVERT: A 87 TRP cc_start: 0.9181 (t-100) cc_final: 0.8210 (t60) REVERT: A 93 MET cc_start: 0.8758 (mmt) cc_final: 0.8520 (mmp) REVERT: A 97 ASP cc_start: 0.9343 (t70) cc_final: 0.9131 (t0) REVERT: A 101 ARG cc_start: 0.9261 (tpp-160) cc_final: 0.8963 (mmm-85) REVERT: A 157 ASP cc_start: 0.7708 (m-30) cc_final: 0.7406 (m-30) REVERT: A 408 TYR cc_start: 0.9189 (m-80) cc_final: 0.8660 (m-80) REVERT: A 424 CYS cc_start: 0.9496 (m) cc_final: 0.9268 (m) REVERT: A 477 MET cc_start: 0.9047 (tpp) cc_final: 0.8564 (tpt) REVERT: A 478 GLU cc_start: 0.9408 (tp30) cc_final: 0.9120 (tp30) REVERT: A 481 ARG cc_start: 0.9107 (ttt-90) cc_final: 0.8905 (ptm-80) REVERT: A 505 PHE cc_start: 0.9322 (m-80) cc_final: 0.9036 (m-80) REVERT: A 515 MET cc_start: 0.8260 (mmt) cc_final: 0.7863 (mmp) REVERT: A 601 MET cc_start: 0.7941 (ttt) cc_final: 0.7151 (tpt) REVERT: A 621 GLN cc_start: 0.6730 (tm-30) cc_final: 0.6352 (tm-30) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1560 time to fit residues: 41.8660 Evaluate side-chains 171 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** 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 = 0.3484 r_free = 0.3484 target = 0.096517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.069543 restraints weight = 44151.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.074057 restraints weight = 19753.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.077126 restraints weight = 11989.921| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 6071 Z= 0.258 Angle : 0.737 7.779 8326 Z= 0.359 Chirality : 0.044 0.186 883 Planarity : 0.006 0.120 1040 Dihedral : 6.995 71.208 821 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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: -1.08 (0.31), residues: 741 helix: -0.01 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -2.17 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 480 HIS 0.010 0.002 HIS A 568 PHE 0.015 0.002 PHE A 295 TYR 0.017 0.002 TYR A 638 ARG 0.005 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9461 (mt0) cc_final: 0.8925 (mt0) REVERT: A 87 TRP cc_start: 0.9196 (t-100) cc_final: 0.8237 (t60) REVERT: A 93 MET cc_start: 0.8840 (mmt) cc_final: 0.8594 (mmp) REVERT: A 97 ASP cc_start: 0.9366 (t70) cc_final: 0.9129 (t0) REVERT: A 101 ARG cc_start: 0.9275 (tpp-160) cc_final: 0.8981 (mmm-85) REVERT: A 127 TYR cc_start: 0.8070 (m-10) cc_final: 0.7670 (m-80) REVERT: A 153 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6586 (tm-30) REVERT: A 190 THR cc_start: 0.9240 (t) cc_final: 0.8654 (t) REVERT: A 408 TYR cc_start: 0.9076 (m-80) cc_final: 0.8510 (m-80) REVERT: A 420 PHE cc_start: 0.8988 (t80) cc_final: 0.8786 (t80) REVERT: A 424 CYS cc_start: 0.9528 (m) cc_final: 0.9310 (m) REVERT: A 477 MET cc_start: 0.9129 (tpp) cc_final: 0.8590 (tpt) REVERT: A 481 ARG cc_start: 0.9137 (ttt-90) cc_final: 0.8790 (ttt-90) REVERT: A 515 MET cc_start: 0.8360 (mmt) cc_final: 0.7897 (mmp) REVERT: A 592 CYS cc_start: 0.9184 (m) cc_final: 0.8960 (m) REVERT: A 601 MET cc_start: 0.8135 (ttt) cc_final: 0.7279 (tpt) REVERT: A 659 LEU cc_start: 0.8539 (pp) cc_final: 0.8319 (pp) REVERT: A 737 GLN cc_start: 0.9341 (tm-30) cc_final: 0.8963 (tp40) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1542 time to fit residues: 38.4203 Evaluate side-chains 165 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 0.4980 chunk 4 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN A 404 GLN A 612 ASN ** A 690 GLN ** 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 = 0.3523 r_free = 0.3523 target = 0.098999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.074414 restraints weight = 25771.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.078204 restraints weight = 14221.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.080882 restraints weight = 9456.806| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6071 Z= 0.205 Angle : 0.732 8.081 8326 Z= 0.355 Chirality : 0.043 0.186 883 Planarity : 0.006 0.138 1040 Dihedral : 6.917 78.072 821 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.18 % Allowed : 1.96 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.31), residues: 741 helix: 0.17 (0.23), residues: 500 sheet: None (None), residues: 0 loop : -1.96 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 215 HIS 0.007 0.001 HIS A 568 PHE 0.048 0.002 PHE A 295 TYR 0.015 0.002 TYR A 638 ARG 0.005 0.000 ARG A 720 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9453 (mt0) cc_final: 0.8888 (mt0) REVERT: A 87 TRP cc_start: 0.9137 (t-100) cc_final: 0.8328 (t-100) REVERT: A 93 MET cc_start: 0.8758 (mmt) cc_final: 0.8528 (mmp) REVERT: A 97 ASP cc_start: 0.9334 (t70) cc_final: 0.9109 (t0) REVERT: A 101 ARG cc_start: 0.9257 (tpp-160) cc_final: 0.8965 (mmm-85) REVERT: A 127 TYR cc_start: 0.8078 (m-10) cc_final: 0.7724 (m-80) REVERT: A 175 MET cc_start: 0.8354 (mpp) cc_final: 0.8021 (mpp) REVERT: A 190 THR cc_start: 0.9274 (t) cc_final: 0.8939 (t) REVERT: A 371 PHE cc_start: 0.9104 (t80) cc_final: 0.8854 (t80) REVERT: A 408 TYR cc_start: 0.9011 (m-80) cc_final: 0.8585 (m-80) REVERT: A 414 LEU cc_start: 0.9224 (tt) cc_final: 0.8979 (tt) REVERT: A 477 MET cc_start: 0.9072 (tpp) cc_final: 0.8654 (tpt) REVERT: A 505 PHE cc_start: 0.9301 (m-80) cc_final: 0.9007 (m-80) REVERT: A 515 MET cc_start: 0.8302 (mmt) cc_final: 0.7848 (mmp) REVERT: A 592 CYS cc_start: 0.9190 (m) cc_final: 0.8934 (m) REVERT: A 601 MET cc_start: 0.8092 (ttt) cc_final: 0.7220 (tpt) outliers start: 1 outliers final: 1 residues processed: 184 average time/residue: 0.1468 time to fit residues: 37.0292 Evaluate side-chains 159 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 41 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 68 optimal weight: 0.4980 chunk 20 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN A 404 GLN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** 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 = 0.3532 r_free = 0.3532 target = 0.099345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.072940 restraints weight = 34060.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.077191 restraints weight = 16926.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.080279 restraints weight = 10774.813| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6071 Z= 0.198 Angle : 0.702 7.654 8326 Z= 0.340 Chirality : 0.043 0.185 883 Planarity : 0.005 0.092 1040 Dihedral : 6.754 78.767 821 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: -0.62 (0.31), residues: 741 helix: 0.36 (0.24), residues: 493 sheet: None (None), residues: 0 loop : -1.93 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 195 HIS 0.005 0.001 HIS A 305 PHE 0.026 0.001 PHE A 295 TYR 0.014 0.002 TYR A 127 ARG 0.006 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9493 (mt0) cc_final: 0.8931 (mt0) REVERT: A 87 TRP cc_start: 0.9196 (t-100) cc_final: 0.8383 (t-100) REVERT: A 93 MET cc_start: 0.8804 (mmt) cc_final: 0.8575 (mmp) REVERT: A 97 ASP cc_start: 0.9332 (t70) cc_final: 0.9118 (t0) REVERT: A 101 ARG cc_start: 0.9259 (tpp-160) cc_final: 0.8942 (mmm-85) REVERT: A 190 THR cc_start: 0.9303 (t) cc_final: 0.8972 (t) REVERT: A 408 TYR cc_start: 0.9044 (m-80) cc_final: 0.8582 (m-80) REVERT: A 426 TRP cc_start: 0.9356 (t60) cc_final: 0.9008 (t60) REVERT: A 430 MET cc_start: 0.8974 (mmp) cc_final: 0.8659 (mmm) REVERT: A 461 PHE cc_start: 0.9202 (m-80) cc_final: 0.8892 (m-80) REVERT: A 477 MET cc_start: 0.9107 (tpp) cc_final: 0.8584 (tpt) REVERT: A 515 MET cc_start: 0.8307 (mmt) cc_final: 0.7839 (mmp) REVERT: A 592 CYS cc_start: 0.9158 (m) cc_final: 0.8907 (m) REVERT: A 601 MET cc_start: 0.8151 (ttt) cc_final: 0.7251 (tpt) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1389 time to fit residues: 34.2601 Evaluate side-chains 159 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 404 GLN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** 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 = 0.3494 r_free = 0.3494 target = 0.096928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.068950 restraints weight = 39412.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.073336 restraints weight = 18833.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.076350 restraints weight = 11834.878| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 6071 Z= 0.273 Angle : 0.738 6.943 8326 Z= 0.356 Chirality : 0.044 0.182 883 Planarity : 0.005 0.076 1040 Dihedral : 6.949 83.311 821 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -0.50 (0.32), residues: 741 helix: 0.47 (0.24), residues: 493 sheet: None (None), residues: 0 loop : -1.91 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 195 HIS 0.004 0.001 HIS A 305 PHE 0.019 0.002 PHE A 496 TYR 0.016 0.002 TYR A 173 ARG 0.006 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9455 (mt0) cc_final: 0.8835 (mt0) REVERT: A 87 TRP cc_start: 0.9205 (t-100) cc_final: 0.8465 (t-100) REVERT: A 93 MET cc_start: 0.8832 (mmt) cc_final: 0.8612 (mmp) REVERT: A 97 ASP cc_start: 0.9365 (t70) cc_final: 0.9136 (t0) REVERT: A 101 ARG cc_start: 0.9330 (tpp-160) cc_final: 0.9007 (mmm-85) REVERT: A 127 TYR cc_start: 0.7889 (m-10) cc_final: 0.7516 (m-80) REVERT: A 408 TYR cc_start: 0.8921 (m-80) cc_final: 0.8585 (m-80) REVERT: A 424 CYS cc_start: 0.9538 (m) cc_final: 0.9305 (m) REVERT: A 461 PHE cc_start: 0.9250 (m-80) cc_final: 0.9008 (m-80) REVERT: A 477 MET cc_start: 0.9081 (tpp) cc_final: 0.8728 (tpt) REVERT: A 592 CYS cc_start: 0.9179 (m) cc_final: 0.8944 (m) REVERT: A 601 MET cc_start: 0.8115 (ttt) cc_final: 0.7307 (tpt) REVERT: A 683 LEU cc_start: 0.9386 (mm) cc_final: 0.9113 (mm) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1365 time to fit residues: 33.0101 Evaluate side-chains 154 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 10 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN A 404 GLN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** 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 = 0.3535 r_free = 0.3535 target = 0.099601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.073231 restraints weight = 25803.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.076941 restraints weight = 14557.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.079657 restraints weight = 9895.892| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6071 Z= 0.195 Angle : 0.734 8.988 8326 Z= 0.350 Chirality : 0.043 0.174 883 Planarity : 0.008 0.218 1040 Dihedral : 7.356 82.238 821 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: -0.45 (0.31), residues: 741 helix: 0.55 (0.24), residues: 488 sheet: None (None), residues: 0 loop : -1.96 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 195 HIS 0.005 0.001 HIS A 568 PHE 0.018 0.001 PHE A 496 TYR 0.014 0.002 TYR A 30 ARG 0.004 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9492 (mt0) cc_final: 0.8927 (mt0) REVERT: A 87 TRP cc_start: 0.9164 (t-100) cc_final: 0.8415 (t-100) REVERT: A 97 ASP cc_start: 0.9341 (t70) cc_final: 0.9104 (t0) REVERT: A 101 ARG cc_start: 0.9307 (tpp-160) cc_final: 0.8991 (mmm-85) REVERT: A 127 TYR cc_start: 0.7901 (m-10) cc_final: 0.7532 (m-80) REVERT: A 190 THR cc_start: 0.9302 (t) cc_final: 0.8973 (t) REVERT: A 305 HIS cc_start: 0.8011 (t-90) cc_final: 0.7229 (t-90) REVERT: A 371 PHE cc_start: 0.9228 (t80) cc_final: 0.8917 (t80) REVERT: A 408 TYR cc_start: 0.8911 (m-80) cc_final: 0.8545 (m-80) REVERT: A 424 CYS cc_start: 0.9525 (m) cc_final: 0.9294 (m) REVERT: A 461 PHE cc_start: 0.9233 (m-80) cc_final: 0.8938 (m-80) REVERT: A 477 MET cc_start: 0.9032 (tpp) cc_final: 0.8553 (tpt) REVERT: A 515 MET cc_start: 0.8187 (mmt) cc_final: 0.7612 (mmp) REVERT: A 563 LEU cc_start: 0.7121 (mt) cc_final: 0.6876 (mt) REVERT: A 592 CYS cc_start: 0.9117 (m) cc_final: 0.8845 (m) REVERT: A 601 MET cc_start: 0.8108 (ttt) cc_final: 0.7216 (tpt) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1338 time to fit residues: 33.0089 Evaluate side-chains 155 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 404 GLN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** 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 = 0.3518 r_free = 0.3518 target = 0.098522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.070375 restraints weight = 37006.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.074843 restraints weight = 18284.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.077800 restraints weight = 11589.116| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6071 Z= 0.234 Angle : 0.761 13.052 8326 Z= 0.363 Chirality : 0.043 0.190 883 Planarity : 0.009 0.250 1040 Dihedral : 7.492 89.435 821 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: -0.37 (0.32), residues: 741 helix: 0.58 (0.24), residues: 491 sheet: None (None), residues: 0 loop : -1.87 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 195 HIS 0.004 0.001 HIS A 568 PHE 0.022 0.002 PHE A 467 TYR 0.024 0.002 TYR A 462 ARG 0.004 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9439 (mt0) cc_final: 0.8834 (mt0) REVERT: A 87 TRP cc_start: 0.9204 (t-100) cc_final: 0.8431 (t-100) REVERT: A 97 ASP cc_start: 0.9373 (t70) cc_final: 0.9112 (t0) REVERT: A 101 ARG cc_start: 0.9327 (tpp-160) cc_final: 0.9004 (mmm-85) REVERT: A 127 TYR cc_start: 0.8007 (m-10) cc_final: 0.7637 (m-80) REVERT: A 190 THR cc_start: 0.9305 (t) cc_final: 0.8991 (t) REVERT: A 371 PHE cc_start: 0.9249 (t80) cc_final: 0.8934 (t80) REVERT: A 408 TYR cc_start: 0.8842 (m-80) cc_final: 0.8515 (m-80) REVERT: A 424 CYS cc_start: 0.9523 (m) cc_final: 0.9296 (m) REVERT: A 426 TRP cc_start: 0.9417 (t60) cc_final: 0.8773 (t60) REVERT: A 461 PHE cc_start: 0.9290 (m-80) cc_final: 0.8983 (m-80) REVERT: A 477 MET cc_start: 0.9085 (tpp) cc_final: 0.8720 (tpt) REVERT: A 536 PHE cc_start: 0.9579 (m-80) cc_final: 0.9220 (m-80) REVERT: A 592 CYS cc_start: 0.8947 (m) cc_final: 0.8712 (m) REVERT: A 601 MET cc_start: 0.8212 (ttt) cc_final: 0.7359 (tpt) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1316 time to fit residues: 31.8909 Evaluate side-chains 155 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 13 optimal weight: 0.0270 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 30.0000 chunk 56 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 1.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** 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 = 0.3519 r_free = 0.3519 target = 0.098579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.070811 restraints weight = 34311.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.075046 restraints weight = 17593.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.077973 restraints weight = 11353.333| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 6071 Z= 0.233 Angle : 0.766 15.638 8326 Z= 0.367 Chirality : 0.044 0.170 883 Planarity : 0.010 0.298 1040 Dihedral : 7.508 87.931 821 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.32), residues: 741 helix: 0.63 (0.24), residues: 488 sheet: None (None), residues: 0 loop : -1.86 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 195 HIS 0.004 0.001 HIS A 89 PHE 0.018 0.001 PHE A 496 TYR 0.018 0.002 TYR A 362 ARG 0.003 0.000 ARG A 703 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9502 (mt0) cc_final: 0.8813 (mt0) REVERT: A 87 TRP cc_start: 0.9199 (t-100) cc_final: 0.8428 (t-100) REVERT: A 93 MET cc_start: 0.8895 (mmt) cc_final: 0.8633 (mmp) REVERT: A 97 ASP cc_start: 0.9353 (t70) cc_final: 0.9135 (t0) REVERT: A 101 ARG cc_start: 0.9325 (tpp-160) cc_final: 0.9002 (mmm-85) REVERT: A 127 TYR cc_start: 0.8042 (m-10) cc_final: 0.7713 (m-80) REVERT: A 190 THR cc_start: 0.9313 (t) cc_final: 0.9005 (t) REVERT: A 371 PHE cc_start: 0.9249 (t80) cc_final: 0.8949 (t80) REVERT: A 408 TYR cc_start: 0.8812 (m-80) cc_final: 0.8528 (m-80) REVERT: A 424 CYS cc_start: 0.9514 (m) cc_final: 0.9269 (m) REVERT: A 461 PHE cc_start: 0.9240 (m-80) cc_final: 0.8965 (m-80) REVERT: A 477 MET cc_start: 0.9079 (tpp) cc_final: 0.8714 (tpp) REVERT: A 592 CYS cc_start: 0.9008 (m) cc_final: 0.8779 (m) REVERT: A 601 MET cc_start: 0.8198 (ttt) cc_final: 0.7359 (tpt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1282 time to fit residues: 31.5969 Evaluate side-chains 152 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 20 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN A 404 GLN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** 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 = 0.3465 r_free = 0.3465 target = 0.095225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.068784 restraints weight = 42711.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.073044 restraints weight = 19841.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.076096 restraints weight = 12247.591| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 6071 Z= 0.322 Angle : 0.823 16.268 8326 Z= 0.394 Chirality : 0.045 0.180 883 Planarity : 0.009 0.248 1040 Dihedral : 7.469 84.146 821 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: -0.27 (0.32), residues: 741 helix: 0.60 (0.24), residues: 491 sheet: None (None), residues: 0 loop : -1.69 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 599 HIS 0.004 0.001 HIS A 631 PHE 0.020 0.002 PHE A 467 TYR 0.027 0.002 TYR A 462 ARG 0.012 0.001 ARG A 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2096.90 seconds wall clock time: 38 minutes 17.50 seconds (2297.50 seconds total)