Starting phenix.real_space_refine on Sun Aug 24 02:20:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8avb_15677/08_2025/8avb_15677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avb_15677/08_2025/8avb_15677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8avb_15677/08_2025/8avb_15677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avb_15677/08_2025/8avb_15677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8avb_15677/08_2025/8avb_15677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avb_15677/08_2025/8avb_15677.map" } resolution = 4.43 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= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6823 atoms to isotropic. 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 51 5.16 5 C 6790 2.51 5 N 1778 2.21 5 O 1972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10591 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "B" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4757 Classifications: {'peptide': 593} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555} Chain: "F" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4757 Classifications: {'peptide': 593} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555} Time building chain proxies: 2.06, per 1000 atoms: 0.19 Number of scatterers: 10591 At special positions: 0 Unit cell: (99.66, 137.41, 175.16, 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 51 16.00 O 1972 8.00 N 1778 7.00 C 6790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 410 " distance=2.04 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 526 " distance=2.02 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 496 " distance=2.04 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS F 350 " - pdb=" SG CYS F 410 " distance=2.03 Simple disulfide: pdb=" SG CYS F 411 " - pdb=" SG CYS F 416 " distance=2.02 Simple disulfide: pdb=" SG CYS F 434 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 471 " - pdb=" SG CYS F 526 " distance=2.03 Simple disulfide: pdb=" SG CYS F 486 " - pdb=" SG CYS F 496 " distance=2.03 Simple disulfide: pdb=" SG CYS F 602 " - pdb=" SG CYS F 672 " distance=2.02 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: 0.77 Conformation dependent library (CDL) restraints added in 350.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2538 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 29 sheets defined 10.0% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 23 through 44 Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.564A pdb=" N GLN A 49 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 removed outlier: 3.853A pdb=" N SER A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 116 Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.677A pdb=" N VAL A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 160 Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.855A pdb=" N VAL B 533 " --> pdb=" O ASP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 removed outlier: 3.942A pdb=" N LYS B 735 " --> pdb=" O PRO B 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 375 through 377 No H-bonds generated for 'chain 'F' and resid 375 through 377' Processing helix chain 'F' and resid 528 through 533 removed outlier: 3.821A pdb=" N VAL F 533 " --> pdb=" O ASP F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 731 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 246 removed outlier: 5.590A pdb=" N GLY B 241 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP B 257 " --> pdb=" O GLY B 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 279 through 286 Processing sheet with id=AA4, first strand: chain 'B' and resid 332 through 334 Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 340 Processing sheet with id=AA6, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AA7, first strand: chain 'B' and resid 432 through 436 removed outlier: 3.694A pdb=" N VAL B 487 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 482 through 484 removed outlier: 4.578A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 482 through 484 removed outlier: 4.578A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 539 through 545 removed outlier: 6.016A pdb=" N ASN B 540 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU B 557 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 582 through 586 Processing sheet with id=AB3, first strand: chain 'B' and resid 643 through 648 Processing sheet with id=AB4, first strand: chain 'B' and resid 687 through 694 removed outlier: 6.094A pdb=" N TYR B 677 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 739 through 745 Processing sheet with id=AB6, first strand: chain 'B' and resid 782 through 787 Processing sheet with id=AB7, first strand: chain 'F' and resid 240 through 246 removed outlier: 5.214A pdb=" N GLY F 241 " --> pdb=" O ASP F 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 279 through 286 Processing sheet with id=AB9, first strand: chain 'F' and resid 331 through 333 Processing sheet with id=AC1, first strand: chain 'F' and resid 331 through 333 Processing sheet with id=AC2, first strand: chain 'F' and resid 337 through 339 removed outlier: 6.596A pdb=" N ILE F 338 " --> pdb=" O TYR F 424 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 433 through 436 Processing sheet with id=AC4, first strand: chain 'F' and resid 482 through 484 removed outlier: 4.031A pdb=" N LEU F 462 " --> pdb=" O LYS F 484 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 482 through 484 removed outlier: 4.031A pdb=" N LEU F 462 " --> pdb=" O LYS F 484 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 539 through 545 removed outlier: 3.816A pdb=" N VAL F 541 " --> pdb=" O SER F 555 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER F 555 " --> pdb=" O VAL F 541 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA F 543 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS F 553 " --> pdb=" O ALA F 543 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 582 through 586 Processing sheet with id=AC8, first strand: chain 'F' and resid 643 through 648 Processing sheet with id=AC9, first strand: chain 'F' and resid 690 through 694 removed outlier: 5.576A pdb=" N TYR F 677 " --> pdb=" O VAL F 693 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 739 through 746 Processing sheet with id=AD2, first strand: chain 'F' and resid 782 through 787 removed outlier: 3.839A pdb=" N TYR F 767 " --> pdb=" O VAL F 812 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1140 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: 1.84 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1808 1.32 - 1.46: 3328 1.46 - 1.59: 5659 1.59 - 1.72: 1 1.72 - 1.85: 72 Bond restraints: 10868 Sorted by residual: bond pdb=" CG PRO F 801 " pdb=" CD PRO F 801 " ideal model delta sigma weight residual 1.503 1.191 0.312 3.40e-02 8.65e+02 8.41e+01 bond pdb=" N PRO F 801 " pdb=" CD PRO F 801 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" CB PRO F 801 " pdb=" CG PRO F 801 " ideal model delta sigma weight residual 1.492 1.680 -0.188 5.00e-02 4.00e+02 1.41e+01 bond pdb=" CB ASN A 103 " pdb=" CG ASN A 103 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.66e+00 bond pdb=" N PRO F 801 " pdb=" CA PRO F 801 " ideal model delta sigma weight residual 1.472 1.446 0.025 1.34e-02 5.57e+03 3.61e+00 ... (remaining 10863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.77: 14774 4.77 - 9.54: 33 9.54 - 14.31: 5 14.31 - 19.07: 2 19.07 - 23.84: 1 Bond angle restraints: 14815 Sorted by residual: angle pdb=" N PRO F 801 " pdb=" CD PRO F 801 " pdb=" CG PRO F 801 " ideal model delta sigma weight residual 103.20 86.46 16.74 1.50e+00 4.44e-01 1.25e+02 angle pdb=" CA PRO F 801 " pdb=" N PRO F 801 " pdb=" CD PRO F 801 " ideal model delta sigma weight residual 112.00 97.20 14.80 1.40e+00 5.10e-01 1.12e+02 angle pdb=" CB ARG A 41 " pdb=" CG ARG A 41 " pdb=" CD ARG A 41 " ideal model delta sigma weight residual 111.30 135.14 -23.84 2.30e+00 1.89e-01 1.07e+02 angle pdb=" CA PRO F 801 " pdb=" CB PRO F 801 " pdb=" CG PRO F 801 " ideal model delta sigma weight residual 104.50 93.66 10.84 1.90e+00 2.77e-01 3.26e+01 angle pdb=" N SER A 46 " pdb=" CA SER A 46 " pdb=" C SER A 46 " ideal model delta sigma weight residual 110.80 121.38 -10.58 2.13e+00 2.20e-01 2.47e+01 ... (remaining 14810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6133 17.93 - 35.87: 350 35.87 - 53.80: 57 53.80 - 71.73: 7 71.73 - 89.66: 6 Dihedral angle restraints: 6553 sinusoidal: 2639 harmonic: 3914 Sorted by residual: dihedral pdb=" CB CYS F 411 " pdb=" SG CYS F 411 " pdb=" SG CYS F 416 " pdb=" CB CYS F 416 " ideal model delta sinusoidal sigma weight residual 93.00 42.00 51.00 1 1.00e+01 1.00e-02 3.56e+01 dihedral pdb=" CA PHE B 502 " pdb=" C PHE B 502 " pdb=" N LEU B 503 " pdb=" CA LEU B 503 " ideal model delta harmonic sigma weight residual -180.00 -152.29 -27.71 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 496 " pdb=" CB CYS B 496 " ideal model delta sinusoidal sigma weight residual 93.00 49.96 43.04 1 1.00e+01 1.00e-02 2.58e+01 ... (remaining 6550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1444 0.075 - 0.149: 223 0.149 - 0.224: 8 0.224 - 0.298: 1 0.298 - 0.373: 1 Chirality restraints: 1677 Sorted by residual: chirality pdb=" CA GLN A 96 " pdb=" N GLN A 96 " pdb=" C GLN A 96 " pdb=" CB GLN A 96 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CB ILE F 753 " pdb=" CA ILE F 753 " pdb=" CG1 ILE F 753 " pdb=" CG2 ILE F 753 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA PRO A 90 " pdb=" N PRO A 90 " pdb=" C PRO A 90 " pdb=" CB PRO A 90 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.79e-01 ... (remaining 1674 not shown) Planarity restraints: 1863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 800 " -0.106 5.00e-02 4.00e+02 1.46e-01 3.42e+01 pdb=" N PRO F 801 " 0.252 5.00e-02 4.00e+02 pdb=" CA PRO F 801 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO F 801 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 558 " 0.050 5.00e-02 4.00e+02 7.71e-02 9.51e+00 pdb=" N PRO B 559 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 559 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 559 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 24 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" C ILE A 24 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE A 24 " -0.019 2.00e-02 2.50e+03 pdb=" N GLN A 25 " -0.018 2.00e-02 2.50e+03 ... (remaining 1860 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 320 2.69 - 3.25: 10270 3.25 - 3.80: 17396 3.80 - 4.35: 22860 4.35 - 4.90: 36161 Nonbonded interactions: 87007 Sorted by model distance: nonbonded pdb=" OD1 ASN A 103 " pdb=" OG SER B 505 " model vdw 2.142 3.040 nonbonded pdb=" OG1 THR F 397 " pdb=" O VAL F 425 " model vdw 2.142 3.040 nonbonded pdb=" NE2 GLN A 96 " pdb=" N ILE B 501 " model vdw 2.178 3.200 nonbonded pdb=" NE1 TRP B 644 " pdb=" OE2 GLU B 771 " model vdw 2.182 3.120 nonbonded pdb=" NH1 ARG F 368 " pdb=" OD2 ASP F 406 " model vdw 2.206 3.120 ... (remaining 87002 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'F' } 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 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.270 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 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 : 0.005 0.312 10881 Z= 0.196 Angle : 0.811 23.843 14841 Z= 0.456 Chirality : 0.050 0.373 1677 Planarity : 0.006 0.146 1863 Dihedral : 11.641 89.664 3976 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.40 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: -0.47 (0.23), residues: 1318 helix: -0.94 (0.42), residues: 107 sheet: -0.07 (0.21), residues: 574 loop : -0.27 (0.27), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 41 TYR 0.033 0.002 TYR A 140 PHE 0.016 0.001 PHE B 334 TRP 0.020 0.001 TRP F 366 HIS 0.013 0.001 HIS F 418 Details of bonding type rmsd covalent geometry : bond 0.00480 (10868) covalent geometry : angle 0.81023 (14815) SS BOND : bond 0.00560 ( 13) SS BOND : angle 1.34556 ( 26) hydrogen bonds : bond 0.11505 ( 414) hydrogen bonds : angle 7.59479 ( 1140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 140 TYR cc_start: 0.8697 (m-10) cc_final: 0.8208 (m-10) REVERT: A 149 ARG cc_start: 0.8007 (mtt180) cc_final: 0.7247 (mtp180) REVERT: A 155 GLN cc_start: 0.8374 (tp-100) cc_final: 0.7905 (tp-100) REVERT: B 509 MET cc_start: 0.8881 (pmm) cc_final: 0.8623 (pmm) REVERT: B 638 MET cc_start: 0.9329 (mmp) cc_final: 0.9112 (mmm) REVERT: F 397 THR cc_start: 0.6489 (p) cc_final: 0.6239 (p) REVERT: F 403 PHE cc_start: 0.7248 (m-10) cc_final: 0.6842 (m-80) REVERT: F 638 MET cc_start: 0.9243 (mpp) cc_final: 0.8956 (mpp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0956 time to fit residues: 13.4692 Evaluate side-chains 60 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.0570 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 103 ASN B 267 GLN B 369 ASN ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 461 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.106389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.086318 restraints weight = 108572.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.085724 restraints weight = 92635.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.086160 restraints weight = 76798.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.086184 restraints weight = 76314.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.086210 restraints weight = 72315.549| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10881 Z= 0.150 Angle : 0.605 7.413 14841 Z= 0.317 Chirality : 0.047 0.203 1677 Planarity : 0.005 0.054 1863 Dihedral : 5.479 62.948 1433 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: -0.32 (0.23), residues: 1318 helix: 0.69 (0.50), residues: 108 sheet: -0.06 (0.22), residues: 569 loop : -0.38 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 149 TYR 0.021 0.002 TYR F 494 PHE 0.015 0.001 PHE F 493 TRP 0.026 0.001 TRP F 447 HIS 0.010 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00318 (10868) covalent geometry : angle 0.60376 (14815) SS BOND : bond 0.00371 ( 13) SS BOND : angle 0.95458 ( 26) hydrogen bonds : bond 0.04111 ( 414) hydrogen bonds : angle 6.82916 ( 1140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7262 (mm-40) REVERT: A 140 TYR cc_start: 0.8831 (m-10) cc_final: 0.8325 (m-10) REVERT: A 155 GLN cc_start: 0.8682 (tp-100) cc_final: 0.8267 (tp-100) REVERT: B 244 MET cc_start: 0.6555 (tmm) cc_final: 0.5741 (tpp) REVERT: B 503 LEU cc_start: 0.7588 (tp) cc_final: 0.7362 (tt) REVERT: B 509 MET cc_start: 0.8990 (pmm) cc_final: 0.8785 (pmm) REVERT: B 638 MET cc_start: 0.9259 (mmp) cc_final: 0.9004 (mmm) REVERT: F 367 TRP cc_start: 0.7027 (m100) cc_final: 0.6706 (m100) REVERT: F 397 THR cc_start: 0.6532 (p) cc_final: 0.6259 (p) REVERT: F 403 PHE cc_start: 0.7883 (m-10) cc_final: 0.7509 (m-80) REVERT: F 638 MET cc_start: 0.9202 (mpp) cc_final: 0.8874 (mpp) REVERT: F 733 MET cc_start: 0.9020 (mpp) cc_final: 0.8518 (tpp) outliers start: 1 outliers final: 1 residues processed: 85 average time/residue: 0.0911 time to fit residues: 11.7320 Evaluate side-chains 59 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 117 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS B 724 ASN F 259 GLN ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 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 = 0.4458 r_free = 0.4458 target = 0.100004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.081559 restraints weight = 110703.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.079734 restraints weight = 91944.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.080383 restraints weight = 88119.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.080335 restraints weight = 85332.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.080437 restraints weight = 75196.648| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 10881 Z= 0.260 Angle : 0.757 13.305 14841 Z= 0.398 Chirality : 0.050 0.223 1677 Planarity : 0.006 0.104 1863 Dihedral : 6.000 64.727 1433 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 26.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: -0.93 (0.23), residues: 1318 helix: -0.75 (0.45), residues: 114 sheet: -0.35 (0.22), residues: 544 loop : -0.72 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG F 307 TYR 0.025 0.003 TYR A 82 PHE 0.022 0.002 PHE B 498 TRP 0.022 0.002 TRP F 447 HIS 0.008 0.002 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00541 (10868) covalent geometry : angle 0.75615 (14815) SS BOND : bond 0.00664 ( 13) SS BOND : angle 1.26911 ( 26) hydrogen bonds : bond 0.04898 ( 414) hydrogen bonds : angle 7.71733 ( 1140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7708 (mm-40) REVERT: A 140 TYR cc_start: 0.8734 (m-10) cc_final: 0.8340 (m-10) REVERT: A 149 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7701 (mtp180) REVERT: B 244 MET cc_start: 0.5589 (tmm) cc_final: 0.5263 (tmm) REVERT: B 443 MET cc_start: 0.5455 (tpt) cc_final: 0.5050 (tpt) REVERT: B 447 TRP cc_start: 0.8956 (p-90) cc_final: 0.8626 (p-90) REVERT: B 638 MET cc_start: 0.9166 (mmp) cc_final: 0.8874 (mmm) REVERT: B 647 MET cc_start: 0.5153 (mmp) cc_final: 0.4401 (mmm) REVERT: F 403 PHE cc_start: 0.7278 (m-10) cc_final: 0.6977 (m-80) REVERT: F 478 HIS cc_start: 0.8771 (m-70) cc_final: 0.8534 (m-70) REVERT: F 638 MET cc_start: 0.9197 (mpp) cc_final: 0.8744 (mpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1039 time to fit residues: 11.4967 Evaluate side-chains 58 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 104 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 53 optimal weight: 0.0670 chunk 54 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 465 HIS B 685 HIS ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.102607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.083403 restraints weight = 110227.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.082110 restraints weight = 94883.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.082923 restraints weight = 88225.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.082937 restraints weight = 76470.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.082982 restraints weight = 69495.277| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10881 Z= 0.135 Angle : 0.587 6.703 14841 Z= 0.310 Chirality : 0.047 0.175 1677 Planarity : 0.005 0.050 1863 Dihedral : 5.638 61.059 1433 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: -0.78 (0.24), residues: 1318 helix: -0.14 (0.48), residues: 114 sheet: -0.46 (0.22), residues: 561 loop : -0.51 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 512 TYR 0.014 0.002 TYR F 268 PHE 0.015 0.001 PHE F 334 TRP 0.010 0.001 TRP B 556 HIS 0.006 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00282 (10868) covalent geometry : angle 0.58569 (14815) SS BOND : bond 0.00358 ( 13) SS BOND : angle 0.99222 ( 26) hydrogen bonds : bond 0.03600 ( 414) hydrogen bonds : angle 7.14873 ( 1140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.8566 (m-10) cc_final: 0.8212 (m-10) REVERT: A 155 GLN cc_start: 0.9109 (mp10) cc_final: 0.8334 (tp-100) REVERT: B 244 MET cc_start: 0.6312 (tmm) cc_final: 0.5960 (tmm) REVERT: B 443 MET cc_start: 0.5184 (tpt) cc_final: 0.4634 (tpt) REVERT: B 447 TRP cc_start: 0.8859 (p-90) cc_final: 0.8554 (p-90) REVERT: B 638 MET cc_start: 0.9106 (mmp) cc_final: 0.8808 (mmm) REVERT: B 647 MET cc_start: 0.5861 (mmp) cc_final: 0.5337 (mmm) REVERT: F 403 PHE cc_start: 0.7284 (m-10) cc_final: 0.7009 (m-80) REVERT: F 478 HIS cc_start: 0.8677 (m-70) cc_final: 0.8431 (m-70) REVERT: F 638 MET cc_start: 0.9225 (mpp) cc_final: 0.8713 (mpp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0840 time to fit residues: 10.1234 Evaluate side-chains 60 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 GLN A 103 ASN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN B 478 HIS ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 ASN ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.095891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.077774 restraints weight = 112292.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.075768 restraints weight = 81566.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.075443 restraints weight = 90438.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.075559 restraints weight = 94232.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.075669 restraints weight = 83904.850| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 10881 Z= 0.302 Angle : 0.834 16.862 14841 Z= 0.438 Chirality : 0.053 0.289 1677 Planarity : 0.007 0.103 1863 Dihedral : 6.394 62.059 1433 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 32.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: -1.48 (0.23), residues: 1318 helix: -1.55 (0.43), residues: 113 sheet: -0.76 (0.22), residues: 533 loop : -0.95 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 368 TYR 0.030 0.003 TYR B 507 PHE 0.031 0.003 PHE F 334 TRP 0.026 0.003 TRP F 367 HIS 0.008 0.002 HIS F 417 Details of bonding type rmsd covalent geometry : bond 0.00640 (10868) covalent geometry : angle 0.83248 (14815) SS BOND : bond 0.00775 ( 13) SS BOND : angle 1.41589 ( 26) hydrogen bonds : bond 0.05313 ( 414) hydrogen bonds : angle 8.36963 ( 1140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.8776 (m-10) cc_final: 0.8313 (m-10) REVERT: B 244 MET cc_start: 0.6401 (tmm) cc_final: 0.6028 (tmm) REVERT: B 509 MET cc_start: 0.9285 (pmm) cc_final: 0.9021 (pmm) REVERT: B 638 MET cc_start: 0.9164 (mmp) cc_final: 0.8784 (mmm) REVERT: B 647 MET cc_start: 0.6334 (mmp) cc_final: 0.5860 (mmm) REVERT: F 403 PHE cc_start: 0.7128 (m-10) cc_final: 0.6856 (m-80) REVERT: F 478 HIS cc_start: 0.8591 (m-70) cc_final: 0.8341 (m-70) REVERT: F 638 MET cc_start: 0.9195 (mpp) cc_final: 0.8713 (mpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0909 time to fit residues: 10.3826 Evaluate side-chains 57 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 77 optimal weight: 0.2980 chunk 76 optimal weight: 8.9990 chunk 85 optimal weight: 0.2980 chunk 130 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 109 HIS ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS F 324 GLN ** F 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.097994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.078858 restraints weight = 112315.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.077866 restraints weight = 82768.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.077545 restraints weight = 78941.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.077617 restraints weight = 87671.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.077667 restraints weight = 77710.241| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10881 Z= 0.189 Angle : 0.660 8.590 14841 Z= 0.351 Chirality : 0.049 0.191 1677 Planarity : 0.005 0.060 1863 Dihedral : 6.062 53.101 1433 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 24.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.08 % Allowed : 1.88 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: -1.36 (0.23), residues: 1318 helix: -1.15 (0.43), residues: 114 sheet: -0.75 (0.22), residues: 540 loop : -0.86 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 368 TYR 0.018 0.002 TYR F 302 PHE 0.017 0.002 PHE A 62 TRP 0.038 0.002 TRP B 689 HIS 0.008 0.001 HIS F 465 Details of bonding type rmsd covalent geometry : bond 0.00394 (10868) covalent geometry : angle 0.65866 (14815) SS BOND : bond 0.00468 ( 13) SS BOND : angle 1.24411 ( 26) hydrogen bonds : bond 0.04034 ( 414) hydrogen bonds : angle 7.90333 ( 1140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.8747 (m-10) cc_final: 0.8342 (m-10) REVERT: B 447 TRP cc_start: 0.8928 (p-90) cc_final: 0.8685 (p-90) REVERT: B 509 MET cc_start: 0.9137 (pmm) cc_final: 0.8800 (pmm) REVERT: B 638 MET cc_start: 0.9203 (mmp) cc_final: 0.8889 (mmm) REVERT: B 647 MET cc_start: 0.6933 (mmp) cc_final: 0.6729 (mmm) REVERT: F 403 PHE cc_start: 0.7259 (m-10) cc_final: 0.6986 (m-80) REVERT: F 478 HIS cc_start: 0.7856 (m-70) cc_final: 0.7611 (m90) REVERT: F 638 MET cc_start: 0.9179 (mpp) cc_final: 0.8809 (mpp) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.0722 time to fit residues: 8.3966 Evaluate side-chains 56 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 0.0000 chunk 44 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 14 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 HIS B 363 GLN ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS F 369 ASN ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 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 = 0.4445 r_free = 0.4445 target = 0.098281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.077714 restraints weight = 111275.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.077459 restraints weight = 88948.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.078381 restraints weight = 80985.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.078130 restraints weight = 71658.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.078215 restraints weight = 69045.985| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10881 Z= 0.164 Angle : 0.645 9.928 14841 Z= 0.341 Chirality : 0.048 0.176 1677 Planarity : 0.005 0.064 1863 Dihedral : 5.855 39.459 1433 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: -1.26 (0.23), residues: 1318 helix: -0.80 (0.44), residues: 113 sheet: -0.75 (0.22), residues: 545 loop : -0.78 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 41 TYR 0.016 0.002 TYR F 302 PHE 0.016 0.002 PHE B 498 TRP 0.016 0.001 TRP B 689 HIS 0.005 0.001 HIS F 418 Details of bonding type rmsd covalent geometry : bond 0.00342 (10868) covalent geometry : angle 0.64429 (14815) SS BOND : bond 0.00489 ( 13) SS BOND : angle 1.09313 ( 26) hydrogen bonds : bond 0.03816 ( 414) hydrogen bonds : angle 7.69732 ( 1140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8678 (mtm) cc_final: 0.8471 (mtt) REVERT: A 140 TYR cc_start: 0.8837 (m-10) cc_final: 0.8379 (m-10) REVERT: B 447 TRP cc_start: 0.8871 (p-90) cc_final: 0.8652 (p-90) REVERT: B 509 MET cc_start: 0.9135 (pmm) cc_final: 0.8840 (pmm) REVERT: B 638 MET cc_start: 0.9215 (mmp) cc_final: 0.8899 (mmm) REVERT: F 478 HIS cc_start: 0.7688 (m-70) cc_final: 0.7481 (m90) REVERT: F 638 MET cc_start: 0.9213 (mpp) cc_final: 0.8874 (mpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0835 time to fit residues: 9.6555 Evaluate side-chains 59 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 37 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS F 259 GLN F 369 ASN ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 453 GLN ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.095487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.076261 restraints weight = 112210.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.075134 restraints weight = 76606.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.075266 restraints weight = 80769.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.075151 restraints weight = 83715.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.075199 restraints weight = 76078.021| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10881 Z= 0.229 Angle : 0.719 13.506 14841 Z= 0.380 Chirality : 0.050 0.201 1677 Planarity : 0.006 0.106 1863 Dihedral : 6.153 27.478 1433 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 30.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.66 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: -1.61 (0.23), residues: 1318 helix: -1.62 (0.38), residues: 125 sheet: -0.88 (0.22), residues: 539 loop : -0.99 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 656 TYR 0.026 0.002 TYR B 507 PHE 0.027 0.002 PHE F 403 TRP 0.036 0.002 TRP F 367 HIS 0.006 0.002 HIS F 796 Details of bonding type rmsd covalent geometry : bond 0.00477 (10868) covalent geometry : angle 0.71782 (14815) SS BOND : bond 0.00518 ( 13) SS BOND : angle 1.35897 ( 26) hydrogen bonds : bond 0.04495 ( 414) hydrogen bonds : angle 8.12133 ( 1140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 TYR cc_start: 0.7867 (m-80) cc_final: 0.7387 (m-80) REVERT: A 140 TYR cc_start: 0.8537 (m-10) cc_final: 0.7992 (m-10) REVERT: B 443 MET cc_start: 0.5428 (tpt) cc_final: 0.4380 (tpt) REVERT: B 447 TRP cc_start: 0.8936 (p-90) cc_final: 0.8488 (p-90) REVERT: B 638 MET cc_start: 0.9174 (mmp) cc_final: 0.8743 (mmm) REVERT: F 403 PHE cc_start: 0.7606 (m-80) cc_final: 0.7372 (m-80) REVERT: F 478 HIS cc_start: 0.7666 (m-70) cc_final: 0.7274 (m90) REVERT: F 638 MET cc_start: 0.9229 (mpp) cc_final: 0.8783 (mpp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0828 time to fit residues: 10.1114 Evaluate side-chains 58 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 107 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.4980 chunk 74 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.0270 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN B 412 ASN B 564 ASN B 685 HIS F 369 ASN ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.098029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.079687 restraints weight = 110615.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.078019 restraints weight = 87426.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.078181 restraints weight = 89227.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.078143 restraints weight = 89509.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.078287 restraints weight = 79344.634| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10881 Z= 0.141 Angle : 0.627 7.408 14841 Z= 0.333 Chirality : 0.048 0.186 1677 Planarity : 0.005 0.091 1863 Dihedral : 5.829 26.481 1433 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: -1.37 (0.23), residues: 1318 helix: -0.76 (0.44), residues: 113 sheet: -0.91 (0.22), residues: 543 loop : -0.80 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 41 TYR 0.017 0.002 TYR F 424 PHE 0.015 0.002 PHE A 62 TRP 0.024 0.002 TRP F 367 HIS 0.006 0.001 HIS F 418 Details of bonding type rmsd covalent geometry : bond 0.00299 (10868) covalent geometry : angle 0.62588 (14815) SS BOND : bond 0.00537 ( 13) SS BOND : angle 1.07089 ( 26) hydrogen bonds : bond 0.03751 ( 414) hydrogen bonds : angle 7.61106 ( 1140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8488 (mtm) cc_final: 0.8226 (mtt) REVERT: A 149 ARG cc_start: 0.8801 (mtt180) cc_final: 0.7234 (mtm180) REVERT: B 244 MET cc_start: 0.6780 (tmm) cc_final: 0.6038 (tpp) REVERT: B 443 MET cc_start: 0.4872 (tpt) cc_final: 0.4661 (tpt) REVERT: B 447 TRP cc_start: 0.8883 (p-90) cc_final: 0.8657 (p-90) REVERT: B 638 MET cc_start: 0.9220 (mmp) cc_final: 0.8852 (mmm) REVERT: F 478 HIS cc_start: 0.6687 (m-70) cc_final: 0.6400 (m90) REVERT: F 632 MET cc_start: 0.8478 (tpt) cc_final: 0.8228 (tpt) REVERT: F 638 MET cc_start: 0.9219 (mpp) cc_final: 0.8898 (mpp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0911 time to fit residues: 10.5283 Evaluate side-chains 58 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 21 optimal weight: 30.0000 chunk 8 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 ASN ** F 461 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 = 0.4416 r_free = 0.4416 target = 0.096045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.074351 restraints weight = 110729.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.074898 restraints weight = 98401.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.074934 restraints weight = 81973.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.075028 restraints weight = 76158.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.075081 restraints weight = 73517.676| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10881 Z= 0.191 Angle : 0.677 10.140 14841 Z= 0.361 Chirality : 0.049 0.199 1677 Planarity : 0.006 0.090 1863 Dihedral : 5.963 27.019 1433 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 26.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.59 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: -1.55 (0.23), residues: 1318 helix: -1.41 (0.40), residues: 125 sheet: -0.94 (0.22), residues: 538 loop : -0.88 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 512 TYR 0.027 0.002 TYR A 140 PHE 0.015 0.002 PHE B 498 TRP 0.017 0.002 TRP F 367 HIS 0.005 0.001 HIS F 349 Details of bonding type rmsd covalent geometry : bond 0.00401 (10868) covalent geometry : angle 0.67566 (14815) SS BOND : bond 0.00462 ( 13) SS BOND : angle 1.09710 ( 26) hydrogen bonds : bond 0.04223 ( 414) hydrogen bonds : angle 7.85421 ( 1140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.8650 (m-10) cc_final: 0.8245 (m-10) REVERT: B 244 MET cc_start: 0.7163 (tmm) cc_final: 0.6628 (tpp) REVERT: B 443 MET cc_start: 0.5740 (tpt) cc_final: 0.4851 (tpt) REVERT: B 447 TRP cc_start: 0.8962 (p-90) cc_final: 0.8735 (p-90) REVERT: B 638 MET cc_start: 0.9251 (mmp) cc_final: 0.8850 (mmm) REVERT: F 261 MET cc_start: 0.0074 (pmm) cc_final: -0.0140 (pmm) REVERT: F 462 LEU cc_start: 0.7324 (tp) cc_final: 0.6965 (tp) REVERT: F 478 HIS cc_start: 0.6517 (m-70) cc_final: 0.6247 (m90) REVERT: F 632 MET cc_start: 0.8705 (tpt) cc_final: 0.8436 (tpt) REVERT: F 638 MET cc_start: 0.9180 (mpp) cc_final: 0.8797 (mpp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0860 time to fit residues: 9.7018 Evaluate side-chains 56 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 83 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 100 optimal weight: 30.0000 chunk 78 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN F 369 ASN ** F 461 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 = 0.4469 r_free = 0.4469 target = 0.099149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.075029 restraints weight = 109834.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.076324 restraints weight = 82496.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.077096 restraints weight = 68594.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.077351 restraints weight = 59811.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.077687 restraints weight = 55901.332| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10881 Z= 0.127 Angle : 0.617 7.908 14841 Z= 0.331 Chirality : 0.048 0.187 1677 Planarity : 0.005 0.085 1863 Dihedral : 5.599 26.347 1433 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.24 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: -1.16 (0.23), residues: 1318 helix: -0.36 (0.47), residues: 113 sheet: -0.69 (0.23), residues: 509 loop : -0.80 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 41 TYR 0.015 0.001 TYR A 140 PHE 0.015 0.001 PHE A 62 TRP 0.013 0.001 TRP B 510 HIS 0.005 0.001 HIS F 418 Details of bonding type rmsd covalent geometry : bond 0.00273 (10868) covalent geometry : angle 0.61646 (14815) SS BOND : bond 0.00381 ( 13) SS BOND : angle 0.96123 ( 26) hydrogen bonds : bond 0.03602 ( 414) hydrogen bonds : angle 7.29113 ( 1140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2258.98 seconds wall clock time: 39 minutes 40.88 seconds (2380.88 seconds total)