Starting phenix.real_space_refine on Thu Nov 14 06:17:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfe_34718/11_2024/8hfe_34718.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfe_34718/11_2024/8hfe_34718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfe_34718/11_2024/8hfe_34718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfe_34718/11_2024/8hfe_34718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfe_34718/11_2024/8hfe_34718.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfe_34718/11_2024/8hfe_34718.cif" } resolution = 2.5 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= 0.130 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: 5 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 C 2948 2.51 5 N 682 2.21 5 O 762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4413 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4390 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 528} Chain breaks: 2 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1, 'water': 22} Link IDs: {None: 22} Time building chain proxies: 3.14, per 1000 atoms: 0.71 Number of scatterers: 4413 At special positions: 0 Unit cell: (70.3625, 71.445, 99.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 20 16.00 O 762 8.00 N 682 7.00 C 2948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 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: 1.18 Conformation dependent library (CDL) restraints added in 1.1 seconds 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1010 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 80.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.511A pdb=" N ASP A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.697A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.696A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.839A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 264 through 283 removed outlier: 3.758A pdb=" N THR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 3.956A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.515A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.556A pdb=" N LEU A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 320 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 385 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.552A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.623A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.806A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 604 removed outlier: 3.652A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N HIS A 599 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 602 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.834A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 292 hydrogen bonds defined for protein. 843 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: 1.21 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 649 1.28 - 1.41: 1336 1.41 - 1.55: 2516 1.55 - 1.68: 0 1.68 - 1.81: 31 Bond restraints: 4532 Sorted by residual: bond pdb=" C SER A 480 " pdb=" O SER A 480 " ideal model delta sigma weight residual 1.236 1.143 0.093 1.19e-02 7.06e+03 6.06e+01 bond pdb=" C GLY A 478 " pdb=" O GLY A 478 " ideal model delta sigma weight residual 1.235 1.145 0.090 1.35e-02 5.49e+03 4.46e+01 bond pdb=" CA SER A 480 " pdb=" CB SER A 480 " ideal model delta sigma weight residual 1.530 1.431 0.099 1.63e-02 3.76e+03 3.70e+01 bond pdb=" CA ALA A 477 " pdb=" CB ALA A 477 " ideal model delta sigma weight residual 1.530 1.472 0.058 9.80e-03 1.04e+04 3.51e+01 bond pdb=" C ALA A 476 " pdb=" O ALA A 476 " ideal model delta sigma weight residual 1.236 1.179 0.057 1.32e-02 5.74e+03 1.87e+01 ... (remaining 4527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 6109 2.51 - 5.02: 61 5.02 - 7.54: 12 7.54 - 10.05: 0 10.05 - 12.56: 1 Bond angle restraints: 6183 Sorted by residual: angle pdb=" C GLU A 425 " pdb=" N ALA A 426 " pdb=" CA ALA A 426 " ideal model delta sigma weight residual 120.38 132.94 -12.56 1.37e+00 5.33e-01 8.41e+01 angle pdb=" CA ALA A 426 " pdb=" C ALA A 426 " pdb=" O ALA A 426 " ideal model delta sigma weight residual 120.63 125.86 -5.23 1.08e+00 8.57e-01 2.34e+01 angle pdb=" CA ALA A 477 " pdb=" C ALA A 477 " pdb=" N GLY A 478 " ideal model delta sigma weight residual 115.78 121.39 -5.61 1.35e+00 5.49e-01 1.72e+01 angle pdb=" O PHE A 475 " pdb=" C PHE A 475 " pdb=" N ALA A 476 " ideal model delta sigma weight residual 122.48 117.47 5.01 1.21e+00 6.83e-01 1.71e+01 angle pdb=" CA PHE A 475 " pdb=" C PHE A 475 " pdb=" N ALA A 476 " ideal model delta sigma weight residual 118.47 123.63 -5.16 1.26e+00 6.30e-01 1.68e+01 ... (remaining 6178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.54: 2208 15.54 - 31.08: 229 31.08 - 46.62: 71 46.62 - 62.16: 22 62.16 - 77.70: 2 Dihedral angle restraints: 2532 sinusoidal: 947 harmonic: 1585 Sorted by residual: dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual -180.00 -156.47 -23.53 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -132.76 10.16 0 2.50e+00 1.60e-01 1.65e+01 dihedral pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual 122.80 132.51 -9.71 0 2.50e+00 1.60e-01 1.51e+01 ... (remaining 2529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 662 0.088 - 0.175: 26 0.175 - 0.263: 2 0.263 - 0.350: 0 0.350 - 0.438: 1 Chirality restraints: 691 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CA ILE A 617 " pdb=" N ILE A 617 " pdb=" C ILE A 617 " pdb=" CB ILE A 617 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA SER A 480 " pdb=" N SER A 480 " pdb=" C SER A 480 " pdb=" CB SER A 480 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.14e-01 ... (remaining 688 not shown) Planarity restraints: 752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C ILE A 103 " -0.066 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 475 " 0.012 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C PHE A 475 " -0.039 2.00e-02 2.50e+03 pdb=" O PHE A 475 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 476 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 426 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C ALA A 426 " 0.037 2.00e-02 2.50e+03 pdb=" O ALA A 426 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL A 427 " -0.011 2.00e-02 2.50e+03 ... (remaining 749 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 50 2.65 - 3.21: 4149 3.21 - 3.77: 7111 3.77 - 4.34: 10113 4.34 - 4.90: 16559 Nonbonded interactions: 37982 Sorted by model distance: nonbonded pdb=" OE1 GLU A 113 " pdb=" O HOH A 801 " model vdw 2.082 3.040 nonbonded pdb=" O ALA A 384 " pdb=" O HOH A 802 " model vdw 2.090 3.040 nonbonded pdb=" O HOH A 813 " pdb=" O HOH A 822 " model vdw 2.154 3.040 nonbonded pdb=" O HOH A 814 " pdb=" O HOH A 817 " model vdw 2.164 3.040 nonbonded pdb=" OE2 GLU A 488 " pdb=" O HOH A 803 " model vdw 2.211 3.040 ... (remaining 37977 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.000 Find NCS groups from input model: 0.040 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:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 0.099 4532 Z= 0.295 Angle : 0.664 12.562 6183 Z= 0.404 Chirality : 0.042 0.438 691 Planarity : 0.004 0.045 752 Dihedral : 14.852 77.702 1519 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.23 % Rotamer: Outliers : 1.08 % Allowed : 11.88 % Favored : 87.04 % 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: 1.37 (0.38), residues: 542 helix: 1.34 (0.28), residues: 372 sheet: None (None), residues: 0 loop : 0.12 (0.53), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 128 HIS 0.005 0.001 HIS A 199 PHE 0.012 0.001 PHE A 408 TYR 0.014 0.001 TYR A 84 ARG 0.002 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7653 (mttt) outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 1.2611 time to fit residues: 73.4631 Evaluate side-chains 52 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 350 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4532 Z= 0.261 Angle : 0.568 8.731 6183 Z= 0.300 Chirality : 0.043 0.156 691 Planarity : 0.005 0.046 752 Dihedral : 6.544 59.161 603 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.40 % Favored : 97.42 % Rotamer: Outliers : 2.59 % Allowed : 11.02 % Favored : 86.39 % 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: 1.59 (0.38), residues: 542 helix: 1.49 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.22 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 128 HIS 0.004 0.001 HIS A 228 PHE 0.013 0.002 PHE A 110 TYR 0.017 0.002 TYR A 84 ARG 0.002 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8254 (mmt180) REVERT: A 189 LYS cc_start: 0.8338 (mptt) cc_final: 0.7924 (mmtt) REVERT: A 268 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8327 (p) REVERT: A 341 ARG cc_start: 0.7918 (ttp-170) cc_final: 0.7712 (ttp-110) REVERT: A 581 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7685 (mt0) outliers start: 12 outliers final: 6 residues processed: 58 average time/residue: 1.1789 time to fit residues: 71.3595 Evaluate side-chains 54 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 450 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4532 Z= 0.180 Angle : 0.507 6.914 6183 Z= 0.265 Chirality : 0.040 0.159 691 Planarity : 0.004 0.039 752 Dihedral : 5.766 53.146 597 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.03 % Favored : 97.79 % Rotamer: Outliers : 2.16 % Allowed : 11.88 % Favored : 85.96 % 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: 1.91 (0.38), residues: 542 helix: 1.78 (0.27), residues: 378 sheet: None (None), residues: 0 loop : 0.17 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.002 0.001 HIS A 228 PHE 0.012 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.002 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7558 (t70) cc_final: 0.6974 (t70) REVERT: A 189 LYS cc_start: 0.8387 (mptt) cc_final: 0.7983 (mmtt) REVERT: A 268 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8408 (p) REVERT: A 304 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7254 (mm-30) REVERT: A 459 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7288 (t80) outliers start: 10 outliers final: 4 residues processed: 56 average time/residue: 0.9778 time to fit residues: 57.5867 Evaluate side-chains 52 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4532 Z= 0.199 Angle : 0.515 7.173 6183 Z= 0.270 Chirality : 0.041 0.169 691 Planarity : 0.004 0.039 752 Dihedral : 5.103 50.262 593 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.60 % Rotamer: Outliers : 2.59 % Allowed : 12.10 % Favored : 85.31 % 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: 1.93 (0.37), residues: 542 helix: 1.82 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.12 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.002 0.001 HIS A 228 PHE 0.015 0.001 PHE A 329 TYR 0.018 0.001 TYR A 84 ARG 0.002 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7595 (t70) cc_final: 0.6998 (t70) REVERT: A 189 LYS cc_start: 0.8427 (mptt) cc_final: 0.8034 (mmtt) REVERT: A 254 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7666 (mttt) REVERT: A 268 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8405 (p) REVERT: A 581 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7614 (mt0) REVERT: A 610 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.6779 (mt0) outliers start: 12 outliers final: 6 residues processed: 57 average time/residue: 1.0844 time to fit residues: 64.6487 Evaluate side-chains 54 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 610 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4532 Z= 0.286 Angle : 0.558 7.364 6183 Z= 0.297 Chirality : 0.043 0.170 691 Planarity : 0.004 0.042 752 Dihedral : 5.144 47.386 593 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.23 % Rotamer: Outliers : 2.16 % Allowed : 12.74 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.71 (0.37), residues: 542 helix: 1.67 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.02 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.003 0.001 HIS A 228 PHE 0.016 0.002 PHE A 329 TYR 0.019 0.002 TYR A 84 ARG 0.003 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.8463 (mptt) cc_final: 0.8078 (mmtt) REVERT: A 254 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7774 (mttt) REVERT: A 268 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8378 (p) REVERT: A 581 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7672 (mt0) REVERT: A 610 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.6926 (mt0) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 1.3886 time to fit residues: 74.9799 Evaluate side-chains 53 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 610 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4532 Z= 0.172 Angle : 0.495 5.997 6183 Z= 0.260 Chirality : 0.040 0.184 691 Planarity : 0.004 0.039 752 Dihedral : 4.866 44.615 593 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.60 % Rotamer: Outliers : 2.59 % Allowed : 13.17 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.38), residues: 542 helix: 1.93 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.10 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 128 HIS 0.002 0.001 HIS A 228 PHE 0.020 0.001 PHE A 329 TYR 0.019 0.001 TYR A 84 ARG 0.001 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7567 (t70) cc_final: 0.6977 (t70) REVERT: A 100 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8196 (tm) REVERT: A 268 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8394 (p) REVERT: A 581 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7611 (mt0) outliers start: 12 outliers final: 6 residues processed: 58 average time/residue: 0.9171 time to fit residues: 56.0815 Evaluate side-chains 53 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 535 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4532 Z= 0.193 Angle : 0.505 5.848 6183 Z= 0.266 Chirality : 0.041 0.188 691 Planarity : 0.004 0.039 752 Dihedral : 4.775 41.507 593 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.40 % Favored : 97.42 % Rotamer: Outliers : 3.46 % Allowed : 12.31 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.38), residues: 542 helix: 1.92 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.09 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.002 0.001 HIS A 228 PHE 0.021 0.001 PHE A 329 TYR 0.020 0.001 TYR A 391 ARG 0.001 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7594 (t70) cc_final: 0.6999 (t70) REVERT: A 100 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8192 (tm) REVERT: A 121 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7955 (mmt180) REVERT: A 268 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8367 (p) REVERT: A 610 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.6868 (mt0) outliers start: 16 outliers final: 9 residues processed: 59 average time/residue: 1.1338 time to fit residues: 69.9659 Evaluate side-chains 59 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 610 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4532 Z= 0.195 Angle : 0.505 5.847 6183 Z= 0.266 Chirality : 0.041 0.197 691 Planarity : 0.004 0.039 752 Dihedral : 4.650 35.775 593 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.60 % Rotamer: Outliers : 3.24 % Allowed : 12.74 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.38), residues: 542 helix: 1.94 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.04 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.002 0.001 HIS A 228 PHE 0.023 0.001 PHE A 329 TYR 0.022 0.001 TYR A 391 ARG 0.002 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7595 (t70) cc_final: 0.6999 (t70) REVERT: A 100 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8198 (tm) REVERT: A 121 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7948 (mmt180) REVERT: A 268 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8373 (p) REVERT: A 610 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.6824 (mt0) outliers start: 15 outliers final: 8 residues processed: 57 average time/residue: 1.0663 time to fit residues: 63.5824 Evaluate side-chains 56 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 610 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4532 Z= 0.172 Angle : 0.494 7.235 6183 Z= 0.258 Chirality : 0.040 0.206 691 Planarity : 0.004 0.038 752 Dihedral : 4.504 31.253 593 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.60 % Rotamer: Outliers : 3.24 % Allowed : 12.74 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.38), residues: 542 helix: 2.01 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.02 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.002 0.000 HIS A 228 PHE 0.023 0.001 PHE A 329 TYR 0.026 0.001 TYR A 391 ARG 0.001 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7608 (t70) cc_final: 0.7075 (t70) REVERT: A 100 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8177 (tm) REVERT: A 121 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7885 (mmt180) REVERT: A 189 LYS cc_start: 0.8476 (mptt) cc_final: 0.8060 (mmtt) REVERT: A 268 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8382 (p) REVERT: A 459 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7333 (t80) REVERT: A 509 MET cc_start: 0.8410 (mtm) cc_final: 0.8182 (mtt) REVERT: A 579 SER cc_start: 0.8109 (m) cc_final: 0.7831 (p) REVERT: A 610 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.6794 (mt0) outliers start: 15 outliers final: 9 residues processed: 59 average time/residue: 1.0680 time to fit residues: 66.1669 Evaluate side-chains 62 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 610 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 0.0070 chunk 11 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4532 Z= 0.181 Angle : 0.500 6.823 6183 Z= 0.262 Chirality : 0.040 0.211 691 Planarity : 0.004 0.038 752 Dihedral : 4.463 26.813 593 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.23 % Rotamer: Outliers : 2.81 % Allowed : 13.17 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.38), residues: 542 helix: 2.00 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.03 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.002 0.000 HIS A 228 PHE 0.024 0.001 PHE A 329 TYR 0.031 0.001 TYR A 391 ARG 0.001 0.000 ARG A 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7585 (t70) cc_final: 0.7015 (t70) REVERT: A 100 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8177 (tm) REVERT: A 121 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7926 (mmt180) REVERT: A 189 LYS cc_start: 0.8477 (mptt) cc_final: 0.8061 (mmtt) REVERT: A 268 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8378 (p) REVERT: A 459 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7409 (t80) REVERT: A 509 MET cc_start: 0.8406 (mtm) cc_final: 0.8104 (mtt) REVERT: A 579 SER cc_start: 0.8188 (m) cc_final: 0.7930 (p) REVERT: A 610 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.6784 (mt0) outliers start: 13 outliers final: 8 residues processed: 57 average time/residue: 1.1335 time to fit residues: 67.5436 Evaluate side-chains 61 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 610 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.106215 restraints weight = 5535.556| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.70 r_work: 0.3340 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4532 Z= 0.201 Angle : 0.512 6.803 6183 Z= 0.268 Chirality : 0.041 0.210 691 Planarity : 0.004 0.039 752 Dihedral : 4.493 24.108 593 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.23 % Rotamer: Outliers : 2.81 % Allowed : 13.61 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.38), residues: 542 helix: 1.97 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.02 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 585 HIS 0.002 0.001 HIS A 228 PHE 0.024 0.001 PHE A 329 TYR 0.042 0.002 TYR A 391 ARG 0.002 0.000 ARG A 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1850.93 seconds wall clock time: 34 minutes 13.45 seconds (2053.45 seconds total)