Starting phenix.real_space_refine on Sun Mar 10 23:04:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t6v_10387/03_2024/6t6v_10387_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t6v_10387/03_2024/6t6v_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t6v_10387/03_2024/6t6v_10387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t6v_10387/03_2024/6t6v_10387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t6v_10387/03_2024/6t6v_10387_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t6v_10387/03_2024/6t6v_10387_updated.pdb" } 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 Residue "A ARG 6": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A ASP 724": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5868 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5868 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 745, 5864 Unusual residues: {' CA': 1, 'HEM': 2} Classifications: {'peptide': 742, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 35, 'TRANS': 706, None: 3} Not linked: pdbres="LEU A 743 " pdbres="HEM A 801 " Not linked: pdbres="HEM A 801 " pdbres="HEM A 802 " Not linked: pdbres="HEM A 802 " pdbres=" CA A 803 " 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: 745, 5864 Unusual residues: {' CA': 1, 'HEM': 2} Classifications: {'peptide': 742, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 35, 'TRANS': 706, None: 3} Not linked: pdbres="LEU A 743 " pdbres="HEM A 801 " Not linked: pdbres="HEM A 801 " pdbres="HEM A 802 " Not linked: pdbres="HEM A 802 " pdbres=" CA A 803 " 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: 6063 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: 6.33, per 1000 atoms: 1.08 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 2.2 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... running ksdssp... Secondary structure from input PDB file: 36 helices and 0 sheets defined 61.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 6 through 29 removed outlier: 3.869A pdb=" N LEU A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ILE A 12 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA A 13 " --> pdb=" O PHE A 9 " (cutoff:3.500A) 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 63 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 83 through 101 removed outlier: 3.817A pdb=" N LEU A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 Processing helix chain 'A' and resid 143 through 158 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 164 through 170 removed outlier: 4.012A pdb=" N HIS A 167 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG A 168 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 170 " --> pdb=" O HIS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 198 Processing helix chain 'A' and resid 227 through 252 removed outlier: 3.961A pdb=" N LEU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 308 removed outlier: 4.486A pdb=" N LEU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLY A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LYS A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 354 removed outlier: 3.551A pdb=" N PHE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Proline residue: A 352 - end of helix Processing helix chain 'A' and resid 363 through 389 Processing helix chain 'A' and resid 398 through 401 No H-bonds generated for 'chain 'A' and resid 398 through 401' Processing helix chain 'A' and resid 413 through 437 Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 446 through 460 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 465 Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 494 through 507 Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.945A pdb=" N PHE A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 537 No H-bonds generated for 'chain 'A' and resid 535 through 537' Processing helix chain 'A' and resid 546 through 554 removed outlier: 3.740A pdb=" N SER A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 581 through 584 Processing helix chain 'A' and resid 587 through 600 removed outlier: 3.797A pdb=" N ALA A 597 " --> pdb=" O PHE A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 610 No H-bonds generated for 'chain 'A' and resid 607 through 610' Processing helix chain 'A' and resid 614 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 626 through 636 Processing helix chain 'A' and resid 638 through 653 removed outlier: 4.090A pdb=" N LEU A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 683 through 696 Processing helix chain 'A' and resid 699 through 702 No H-bonds generated for 'chain 'A' and resid 699 through 702' Processing helix chain 'A' and resid 705 through 708 No H-bonds generated for 'chain 'A' and resid 705 through 708' Processing helix chain 'A' and resid 713 through 718 Processing helix chain 'A' and resid 721 through 741 removed outlier: 4.419A pdb=" N VAL A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 849 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: 1.60 Time building geometry restraints manager: 2.62 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: 86.03 - 104.43: 125 104.43 - 122.83: 7606 122.83 - 141.23: 591 141.23 - 159.64: 0 159.64 - 178.04: 4 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: 64 2.54 - 3.13: 4491 3.13 - 3.72: 10167 3.72 - 4.31: 13040 4.31 - 4.90: 20628 Nonbonded interactions: 48390 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 2.440 ... (remaining 48385 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: 0.250 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: 1.070 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 24.210 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.940 ------------------------------------------------------------------------------- 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= 0.613 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 fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 0.681 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: 0.1712 time to fit residues: 45.7148 Evaluate side-chains 161 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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: 5.9990 chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 6071 Z= 0.344 Angle : 0.864 21.908 8326 Z= 0.389 Chirality : 0.045 0.177 883 Planarity : 0.005 0.037 1040 Dihedral : 7.220 78.288 821 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: -1.99 (0.29), residues: 741 helix: -0.80 (0.22), residues: 498 sheet: None (None), residues: 0 loop : -2.24 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 480 HIS 0.008 0.002 HIS A 631 PHE 0.025 0.002 PHE A 727 TYR 0.015 0.002 TYR A 408 ARG 0.002 0.000 ARG A 471 *********************** 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 184 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9179 (m) cc_final: 0.8598 (m) REVERT: A 62 GLN cc_start: 0.9280 (mt0) cc_final: 0.8586 (mt0) REVERT: A 87 TRP cc_start: 0.8985 (t-100) cc_final: 0.8165 (t60) REVERT: A 88 LEU cc_start: 0.9656 (tp) cc_final: 0.9413 (tp) REVERT: A 93 MET cc_start: 0.8751 (mmt) cc_final: 0.8486 (mmp) REVERT: A 101 ARG cc_start: 0.9269 (tpp-160) cc_final: 0.8937 (mmm-85) REVERT: A 153 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6274 (tm-30) REVERT: A 157 ASP cc_start: 0.7818 (m-30) cc_final: 0.6734 (m-30) REVERT: A 371 PHE cc_start: 0.9247 (t80) cc_final: 0.8970 (t80) REVERT: A 406 TYR cc_start: 0.8479 (m-80) cc_final: 0.7885 (m-80) REVERT: A 408 TYR cc_start: 0.9186 (m-80) cc_final: 0.8490 (m-80) REVERT: A 424 CYS cc_start: 0.9478 (m) cc_final: 0.9139 (m) REVERT: A 477 MET cc_start: 0.8774 (tpp) cc_final: 0.8195 (tpp) REVERT: A 481 ARG cc_start: 0.9187 (ttt-90) cc_final: 0.8550 (ptm160) REVERT: A 515 MET cc_start: 0.7885 (mmt) cc_final: 0.7618 (mmp) REVERT: A 528 MET cc_start: 0.8153 (ptt) cc_final: 0.7946 (ptt) REVERT: A 601 MET cc_start: 0.7837 (ttt) cc_final: 0.6974 (mmm) REVERT: A 621 GLN cc_start: 0.7443 (tm-30) cc_final: 0.6997 (tm-30) REVERT: A 659 LEU cc_start: 0.8310 (pp) cc_final: 0.8099 (pp) REVERT: A 663 LEU cc_start: 0.9329 (pp) cc_final: 0.9085 (pp) REVERT: A 737 GLN cc_start: 0.9228 (tm-30) cc_final: 0.8472 (tp40) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1436 time to fit residues: 36.2664 Evaluate side-chains 158 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 6071 Z= 0.312 Angle : 0.756 13.784 8326 Z= 0.349 Chirality : 0.044 0.217 883 Planarity : 0.005 0.039 1040 Dihedral : 7.080 66.106 821 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % 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: -1.16 (0.31), residues: 741 helix: -0.08 (0.23), residues: 500 sheet: None (None), residues: 0 loop : -2.12 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 480 HIS 0.005 0.001 HIS A 568 PHE 0.019 0.002 PHE A 593 TYR 0.017 0.002 TYR A 638 ARG 0.004 0.000 ARG A 413 *********************** 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 183 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9165 (m) cc_final: 0.8556 (m) REVERT: A 62 GLN cc_start: 0.9211 (mt0) cc_final: 0.8467 (mt0) REVERT: A 87 TRP cc_start: 0.9013 (t-100) cc_final: 0.8174 (t60) REVERT: A 88 LEU cc_start: 0.9660 (tp) cc_final: 0.9425 (tp) REVERT: A 93 MET cc_start: 0.8758 (mmt) cc_final: 0.8477 (mmp) REVERT: A 101 ARG cc_start: 0.9269 (tpp-160) cc_final: 0.8996 (mmm-85) REVERT: A 190 THR cc_start: 0.9275 (t) cc_final: 0.8948 (t) REVERT: A 285 TYR cc_start: 0.8325 (m-80) cc_final: 0.8016 (m-80) REVERT: A 406 TYR cc_start: 0.8466 (m-80) cc_final: 0.7985 (m-80) REVERT: A 408 TYR cc_start: 0.9056 (m-80) cc_final: 0.8489 (m-80) REVERT: A 414 LEU cc_start: 0.9262 (tt) cc_final: 0.8918 (tt) REVERT: A 424 CYS cc_start: 0.9499 (m) cc_final: 0.9220 (m) REVERT: A 477 MET cc_start: 0.8785 (tpp) cc_final: 0.8206 (tpp) REVERT: A 478 GLU cc_start: 0.9179 (tp30) cc_final: 0.8942 (tp30) REVERT: A 481 ARG cc_start: 0.9130 (ttt-90) cc_final: 0.8535 (ptm160) REVERT: A 515 MET cc_start: 0.8106 (mmt) cc_final: 0.7779 (mmp) REVERT: A 528 MET cc_start: 0.7879 (ptt) cc_final: 0.7671 (ptt) REVERT: A 621 GLN cc_start: 0.7195 (tm-30) cc_final: 0.6803 (tm-30) REVERT: A 659 LEU cc_start: 0.8281 (pp) cc_final: 0.7811 (pp) REVERT: A 737 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8730 (tp40) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1501 time to fit residues: 37.2576 Evaluate side-chains 159 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN A 672 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6071 Z= 0.223 Angle : 0.692 7.464 8326 Z= 0.328 Chirality : 0.042 0.172 883 Planarity : 0.004 0.038 1040 Dihedral : 6.792 68.862 821 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % 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: -0.58 (0.31), residues: 741 helix: 0.36 (0.24), residues: 487 sheet: None (None), residues: 0 loop : -1.78 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 480 HIS 0.011 0.002 HIS A 568 PHE 0.021 0.002 PHE A 420 TYR 0.023 0.002 TYR A 638 ARG 0.006 0.000 ARG A 720 *********************** 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 184 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9114 (m) cc_final: 0.8483 (m) REVERT: A 62 GLN cc_start: 0.9186 (mt0) cc_final: 0.8512 (mt0) REVERT: A 72 ILE cc_start: 0.9392 (mm) cc_final: 0.9122 (mm) REVERT: A 87 TRP cc_start: 0.8932 (t-100) cc_final: 0.8055 (t60) REVERT: A 88 LEU cc_start: 0.9653 (tp) cc_final: 0.9436 (tp) REVERT: A 93 MET cc_start: 0.8701 (mmt) cc_final: 0.8414 (mmp) REVERT: A 101 ARG cc_start: 0.9275 (tpp-160) cc_final: 0.8992 (mmm-85) REVERT: A 127 TYR cc_start: 0.7949 (m-10) cc_final: 0.7424 (m-80) REVERT: A 190 THR cc_start: 0.9292 (t) cc_final: 0.8960 (t) REVERT: A 295 PHE cc_start: 0.8959 (t80) cc_final: 0.8679 (t80) REVERT: A 371 PHE cc_start: 0.9099 (t80) cc_final: 0.8609 (t80) REVERT: A 406 TYR cc_start: 0.8313 (m-80) cc_final: 0.7951 (m-80) REVERT: A 408 TYR cc_start: 0.8962 (m-80) cc_final: 0.8541 (m-80) REVERT: A 461 PHE cc_start: 0.9149 (m-80) cc_final: 0.8769 (m-80) REVERT: A 477 MET cc_start: 0.8702 (tpp) cc_final: 0.8208 (tpp) REVERT: A 481 ARG cc_start: 0.9025 (ttt-90) cc_final: 0.8478 (ptm160) REVERT: A 515 MET cc_start: 0.8169 (mmt) cc_final: 0.7867 (mmp) REVERT: A 528 MET cc_start: 0.7803 (ptt) cc_final: 0.7584 (ptt) REVERT: A 601 MET cc_start: 0.8085 (ttt) cc_final: 0.7301 (tpt) REVERT: A 612 ASN cc_start: 0.9413 (t0) cc_final: 0.9018 (m-40) REVERT: A 621 GLN cc_start: 0.7071 (tm-30) cc_final: 0.6732 (tm-30) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1511 time to fit residues: 38.1717 Evaluate side-chains 163 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6071 Z= 0.230 Angle : 0.688 7.970 8326 Z= 0.325 Chirality : 0.042 0.189 883 Planarity : 0.004 0.035 1040 Dihedral : 6.700 70.873 821 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % 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: -0.46 (0.31), residues: 741 helix: 0.45 (0.24), residues: 494 sheet: None (None), residues: 0 loop : -1.79 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 480 HIS 0.006 0.002 HIS A 568 PHE 0.032 0.001 PHE A 295 TYR 0.026 0.002 TYR A 306 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 179 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9166 (m) cc_final: 0.8530 (m) REVERT: A 62 GLN cc_start: 0.9000 (mt0) cc_final: 0.8326 (mt0) REVERT: A 87 TRP cc_start: 0.8916 (t-100) cc_final: 0.8043 (t60) REVERT: A 88 LEU cc_start: 0.9655 (tp) cc_final: 0.9448 (tp) REVERT: A 93 MET cc_start: 0.8716 (mmt) cc_final: 0.8440 (mmp) REVERT: A 101 ARG cc_start: 0.9279 (tpp-160) cc_final: 0.9005 (mmm-85) REVERT: A 127 TYR cc_start: 0.7936 (m-10) cc_final: 0.7389 (m-80) REVERT: A 305 HIS cc_start: 0.8102 (t-90) cc_final: 0.7713 (t-90) REVERT: A 404 GLN cc_start: 0.9052 (tt0) cc_final: 0.8783 (tt0) REVERT: A 406 TYR cc_start: 0.8309 (m-80) cc_final: 0.7948 (m-80) REVERT: A 408 TYR cc_start: 0.8865 (m-80) cc_final: 0.8396 (m-80) REVERT: A 461 PHE cc_start: 0.9162 (m-80) cc_final: 0.8723 (m-80) REVERT: A 477 MET cc_start: 0.8696 (tpp) cc_final: 0.8248 (tpp) REVERT: A 481 ARG cc_start: 0.8992 (ttt-90) cc_final: 0.8453 (ptm160) REVERT: A 493 PHE cc_start: 0.8850 (m-10) cc_final: 0.8573 (m-10) REVERT: A 515 MET cc_start: 0.8213 (mmt) cc_final: 0.7864 (mmp) REVERT: A 601 MET cc_start: 0.8082 (ttt) cc_final: 0.7227 (tpt) REVERT: A 612 ASN cc_start: 0.9384 (t0) cc_final: 0.9020 (m-40) REVERT: A 621 GLN cc_start: 0.6739 (tm-30) cc_final: 0.6443 (tm-30) REVERT: A 720 ARG cc_start: 0.8070 (ttt90) cc_final: 0.7683 (ttt90) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1344 time to fit residues: 33.5956 Evaluate side-chains 155 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 213 ASN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6071 Z= 0.234 Angle : 0.680 6.991 8326 Z= 0.322 Chirality : 0.041 0.179 883 Planarity : 0.004 0.034 1040 Dihedral : 6.661 72.938 821 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % 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: -0.14 (0.32), residues: 741 helix: 0.67 (0.24), residues: 489 sheet: None (None), residues: 0 loop : -1.55 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 426 HIS 0.005 0.001 HIS A 568 PHE 0.024 0.001 PHE A 593 TYR 0.014 0.002 TYR A 173 ARG 0.005 0.000 ARG A 720 *********************** 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 fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9173 (m) cc_final: 0.8531 (m) REVERT: A 62 GLN cc_start: 0.8995 (mt0) cc_final: 0.8316 (mt0) REVERT: A 87 TRP cc_start: 0.8915 (t-100) cc_final: 0.8050 (t60) REVERT: A 93 MET cc_start: 0.8716 (mmt) cc_final: 0.8442 (mmp) REVERT: A 101 ARG cc_start: 0.9279 (tpp-160) cc_final: 0.9011 (mmm-85) REVERT: A 190 THR cc_start: 0.9299 (t) cc_final: 0.9017 (t) REVERT: A 305 HIS cc_start: 0.8075 (t-90) cc_final: 0.7689 (t-90) REVERT: A 404 GLN cc_start: 0.9064 (tt0) cc_final: 0.8771 (tt0) REVERT: A 406 TYR cc_start: 0.8217 (m-80) cc_final: 0.7963 (m-80) REVERT: A 408 TYR cc_start: 0.8826 (m-80) cc_final: 0.8322 (m-80) REVERT: A 424 CYS cc_start: 0.9453 (m) cc_final: 0.9228 (m) REVERT: A 461 PHE cc_start: 0.9167 (m-80) cc_final: 0.8697 (m-80) REVERT: A 477 MET cc_start: 0.8726 (tpp) cc_final: 0.8272 (tpp) REVERT: A 481 ARG cc_start: 0.9007 (ttt-90) cc_final: 0.8453 (ptm160) REVERT: A 493 PHE cc_start: 0.8857 (m-10) cc_final: 0.8646 (m-10) REVERT: A 515 MET cc_start: 0.8243 (mmt) cc_final: 0.7864 (mmp) REVERT: A 566 LEU cc_start: 0.8945 (tp) cc_final: 0.8723 (tp) REVERT: A 601 MET cc_start: 0.8111 (ttt) cc_final: 0.7374 (tpt) REVERT: A 612 ASN cc_start: 0.9364 (t0) cc_final: 0.9015 (m-40) REVERT: A 621 GLN cc_start: 0.6817 (tm-30) cc_final: 0.6505 (tm-30) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1333 time to fit residues: 32.6754 Evaluate side-chains 159 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 213 ASN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 6071 Z= 0.341 Angle : 0.747 10.039 8326 Z= 0.348 Chirality : 0.043 0.180 883 Planarity : 0.004 0.037 1040 Dihedral : 6.706 75.829 821 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.31), residues: 741 helix: 0.70 (0.24), residues: 487 sheet: None (None), residues: 0 loop : -1.65 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 426 HIS 0.010 0.002 HIS A 538 PHE 0.017 0.002 PHE A 466 TYR 0.019 0.002 TYR A 479 ARG 0.003 0.000 ARG A 90 *********************** 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 177 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 59 THR cc_start: 0.9205 (m) cc_final: 0.8577 (m) REVERT: A 62 GLN cc_start: 0.9060 (mt0) cc_final: 0.8387 (mt0) REVERT: A 87 TRP cc_start: 0.8964 (t-100) cc_final: 0.8088 (t60) REVERT: A 93 MET cc_start: 0.8795 (mmt) cc_final: 0.8531 (mmp) REVERT: A 101 ARG cc_start: 0.9297 (tpp-160) cc_final: 0.9024 (mmm-85) REVERT: A 190 THR cc_start: 0.9227 (t) cc_final: 0.8952 (t) REVERT: A 305 HIS cc_start: 0.8242 (t-90) cc_final: 0.7841 (t-90) REVERT: A 370 LEU cc_start: 0.9363 (tt) cc_final: 0.9087 (tt) REVERT: A 371 PHE cc_start: 0.9178 (t80) cc_final: 0.8785 (t80) REVERT: A 406 TYR cc_start: 0.8247 (m-80) cc_final: 0.7986 (m-80) REVERT: A 408 TYR cc_start: 0.8711 (m-80) cc_final: 0.8313 (m-80) REVERT: A 416 GLN cc_start: 0.9039 (mt0) cc_final: 0.8583 (mt0) REVERT: A 424 CYS cc_start: 0.9451 (m) cc_final: 0.9218 (m) REVERT: A 461 PHE cc_start: 0.9202 (m-80) cc_final: 0.8749 (m-80) REVERT: A 477 MET cc_start: 0.8834 (tpp) cc_final: 0.8324 (tpp) REVERT: A 481 ARG cc_start: 0.9119 (ttt-90) cc_final: 0.8574 (ptm160) REVERT: A 515 MET cc_start: 0.8336 (mmt) cc_final: 0.7990 (mmp) REVERT: A 590 LEU cc_start: 0.9135 (mm) cc_final: 0.8622 (pp) REVERT: A 601 MET cc_start: 0.8068 (ttt) cc_final: 0.7221 (tpt) REVERT: A 683 LEU cc_start: 0.9432 (mm) cc_final: 0.9215 (mm) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1413 time to fit residues: 34.9826 Evaluate side-chains 158 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 35 optimal weight: 0.0060 chunk 6 optimal weight: 4.9990 chunk 56 optimal weight: 0.0870 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- 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 213 ASN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6071 Z= 0.193 Angle : 0.709 9.859 8326 Z= 0.327 Chirality : 0.042 0.176 883 Planarity : 0.004 0.033 1040 Dihedral : 6.600 73.447 821 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % 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: -0.02 (0.31), residues: 741 helix: 0.75 (0.24), residues: 483 sheet: None (None), residues: 0 loop : -1.43 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 215 HIS 0.005 0.001 HIS A 568 PHE 0.018 0.001 PHE A 466 TYR 0.022 0.002 TYR A 306 ARG 0.003 0.000 ARG A 720 *********************** 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 182 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9132 (m) cc_final: 0.8487 (m) REVERT: A 62 GLN cc_start: 0.8981 (mt0) cc_final: 0.8259 (mt0) REVERT: A 87 TRP cc_start: 0.8824 (t-100) cc_final: 0.8134 (t-100) REVERT: A 93 MET cc_start: 0.8626 (mmt) cc_final: 0.8415 (mmp) REVERT: A 101 ARG cc_start: 0.9300 (tpp-160) cc_final: 0.8892 (tpp80) REVERT: A 190 THR cc_start: 0.9257 (t) cc_final: 0.8999 (t) REVERT: A 371 PHE cc_start: 0.9227 (t80) cc_final: 0.8987 (t80) REVERT: A 408 TYR cc_start: 0.8683 (m-80) cc_final: 0.8224 (m-80) REVERT: A 424 CYS cc_start: 0.9431 (m) cc_final: 0.9228 (m) REVERT: A 461 PHE cc_start: 0.9158 (m-80) cc_final: 0.8705 (m-80) REVERT: A 477 MET cc_start: 0.8762 (tpp) cc_final: 0.8383 (tpt) REVERT: A 481 ARG cc_start: 0.9000 (ttt-90) cc_final: 0.8420 (ptm160) REVERT: A 515 MET cc_start: 0.8180 (mmt) cc_final: 0.7789 (mmp) REVERT: A 563 LEU cc_start: 0.6842 (mt) cc_final: 0.6497 (mt) REVERT: A 601 MET cc_start: 0.7984 (ttt) cc_final: 0.7121 (tpt) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1476 time to fit residues: 36.7353 Evaluate side-chains 165 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.2980 chunk 66 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 213 ASN A 305 HIS ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6071 Z= 0.225 Angle : 0.698 7.869 8326 Z= 0.326 Chirality : 0.042 0.177 883 Planarity : 0.004 0.034 1040 Dihedral : 6.578 74.126 821 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.32), residues: 741 helix: 0.87 (0.24), residues: 482 sheet: None (None), residues: 0 loop : -1.42 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 215 HIS 0.006 0.001 HIS A 75 PHE 0.020 0.001 PHE A 466 TYR 0.030 0.002 TYR A 462 ARG 0.005 0.000 ARG A 720 *********************** 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 181 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9170 (m) cc_final: 0.8488 (m) REVERT: A 62 GLN cc_start: 0.9027 (mt0) cc_final: 0.8334 (mt0) REVERT: A 87 TRP cc_start: 0.8874 (t-100) cc_final: 0.8165 (t-100) REVERT: A 93 MET cc_start: 0.8692 (mmt) cc_final: 0.8481 (mmp) REVERT: A 97 ASP cc_start: 0.9298 (t0) cc_final: 0.8990 (t0) REVERT: A 101 ARG cc_start: 0.9306 (tpp-160) cc_final: 0.9007 (mmm-85) REVERT: A 157 ASP cc_start: 0.7898 (m-30) cc_final: 0.7508 (m-30) REVERT: A 190 THR cc_start: 0.9275 (t) cc_final: 0.9002 (t) REVERT: A 404 GLN cc_start: 0.9026 (tt0) cc_final: 0.8325 (tm-30) REVERT: A 408 TYR cc_start: 0.8714 (m-80) cc_final: 0.8227 (m-80) REVERT: A 424 CYS cc_start: 0.9432 (m) cc_final: 0.9220 (m) REVERT: A 461 PHE cc_start: 0.9160 (m-80) cc_final: 0.8733 (m-80) REVERT: A 477 MET cc_start: 0.8813 (tpp) cc_final: 0.8268 (tpp) REVERT: A 481 ARG cc_start: 0.9057 (ttt-90) cc_final: 0.8419 (ptm160) REVERT: A 515 MET cc_start: 0.8174 (mmt) cc_final: 0.7784 (mmp) REVERT: A 563 LEU cc_start: 0.7029 (mt) cc_final: 0.6748 (mt) REVERT: A 601 MET cc_start: 0.7995 (ttt) cc_final: 0.7129 (tpt) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1316 time to fit residues: 33.2640 Evaluate side-chains 159 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 45 optimal weight: 9.9990 chunk 35 optimal weight: 0.0070 chunk 46 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 213 ASN ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** A 385 ASN ** 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 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6071 Z= 0.191 Angle : 0.701 8.252 8326 Z= 0.325 Chirality : 0.042 0.187 883 Planarity : 0.004 0.032 1040 Dihedral : 6.524 73.643 821 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.31), residues: 741 helix: 0.90 (0.24), residues: 471 sheet: None (None), residues: 0 loop : -1.50 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 215 HIS 0.007 0.001 HIS A 538 PHE 0.022 0.001 PHE A 492 TYR 0.029 0.002 TYR A 462 ARG 0.004 0.000 ARG A 720 ********************** 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 182 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9196 (m) cc_final: 0.8541 (m) REVERT: A 62 GLN cc_start: 0.8988 (mt0) cc_final: 0.8348 (mt0) REVERT: A 87 TRP cc_start: 0.8829 (t-100) cc_final: 0.8125 (t-100) REVERT: A 97 ASP cc_start: 0.9278 (t0) cc_final: 0.8217 (t0) REVERT: A 101 ARG cc_start: 0.9294 (tpp-160) cc_final: 0.8872 (tpp80) REVERT: A 127 TYR cc_start: 0.7640 (m-10) cc_final: 0.7378 (m-10) REVERT: A 157 ASP cc_start: 0.7867 (m-30) cc_final: 0.7474 (m-30) REVERT: A 190 THR cc_start: 0.9266 (t) cc_final: 0.8985 (t) REVERT: A 338 TRP cc_start: 0.9382 (p-90) cc_final: 0.9053 (p-90) REVERT: A 371 PHE cc_start: 0.9179 (t80) cc_final: 0.8872 (t80) REVERT: A 404 GLN cc_start: 0.8943 (tt0) cc_final: 0.8397 (tm-30) REVERT: A 408 TYR cc_start: 0.8810 (m-80) cc_final: 0.8427 (m-80) REVERT: A 424 CYS cc_start: 0.9413 (m) cc_final: 0.9172 (m) REVERT: A 426 TRP cc_start: 0.9152 (t60) cc_final: 0.8794 (t60) REVERT: A 461 PHE cc_start: 0.9135 (m-80) cc_final: 0.8745 (m-80) REVERT: A 477 MET cc_start: 0.8601 (tpp) cc_final: 0.8378 (tpt) REVERT: A 478 GLU cc_start: 0.9001 (tp30) cc_final: 0.8791 (tp30) REVERT: A 481 ARG cc_start: 0.8986 (ttt-90) cc_final: 0.8341 (ptm160) REVERT: A 493 PHE cc_start: 0.8550 (m-80) cc_final: 0.8095 (m-80) REVERT: A 515 MET cc_start: 0.8157 (mmt) cc_final: 0.7764 (mmp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1413 time to fit residues: 35.5940 Evaluate side-chains 161 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 0.0070 chunk 42 optimal weight: 7.9990 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 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 = 0.3476 r_free = 0.3476 target = 0.096172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.070993 restraints weight = 28999.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.074480 restraints weight = 15627.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.077244 restraints weight = 10503.118| |-----------------------------------------------------------------------------| 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: 0.8034 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 0.100 6071 Z= 0.323 Angle : 0.740 8.772 8326 Z= 0.351 Chirality : 0.043 0.184 883 Planarity : 0.004 0.035 1040 Dihedral : 6.743 76.069 821 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 0.08 (0.32), residues: 741 helix: 0.94 (0.25), residues: 473 sheet: None (None), residues: 0 loop : -1.54 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 215 HIS 0.005 0.001 HIS A 538 PHE 0.032 0.002 PHE A 467 TYR 0.030 0.002 TYR A 462 ARG 0.005 0.000 ARG A 720 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1516.51 seconds wall clock time: 28 minutes 29.99 seconds (1709.99 seconds total)