Starting phenix.real_space_refine on Fri Dec 27 11:45:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnd_34911/12_2024/8hnd_34911.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnd_34911/12_2024/8hnd_34911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hnd_34911/12_2024/8hnd_34911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnd_34911/12_2024/8hnd_34911.map" model { file = "/net/cci-nas-00/data/ceres_data/8hnd_34911/12_2024/8hnd_34911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnd_34911/12_2024/8hnd_34911.cif" } resolution = 3.19 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= 0.002 sd= 0.122 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 2879 2.51 5 N 685 2.21 5 O 770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4370 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4304 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 19, 'TRANS': 540} Chain breaks: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'FY5': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.22, per 1000 atoms: 0.74 Number of scatterers: 4370 At special positions: 0 Unit cell: (56.852, 68.036, 103.452, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 770 8.00 N 685 7.00 C 2879 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.02 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.02 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 802 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 532.9 milliseconds 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1018 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 67.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 27 through 50 removed outlier: 4.176A pdb=" N LEU A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 60 removed outlier: 3.641A pdb=" N ARG A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 86 removed outlier: 4.090A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.817A pdb=" N VAL A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 204 through 217 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 258 through 274 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 325 through 335 Processing helix chain 'A' and resid 335 through 367 removed outlier: 4.766A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 381 removed outlier: 3.622A pdb=" N ALA A 374 " --> pdb=" O PRO A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.728A pdb=" N ILE A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 423 removed outlier: 3.538A pdb=" N LYS A 409 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.742A pdb=" N LEU A 512 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 513 " --> pdb=" O THR A 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 513' Processing helix chain 'A' and resid 527 through 550 removed outlier: 3.948A pdb=" N TYR A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 562 removed outlier: 3.507A pdb=" N HIS A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 567 through 598 Proline residue: A 588 - end of helix Processing helix chain 'A' and resid 617 through 651 Processing sheet with id=AA1, first strand: chain 'A' and resid 473 through 475 removed outlier: 3.870A pdb=" N SER A 491 " --> pdb=" O TYR A 502 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 599 through 604 removed outlier: 6.984A pdb=" N CYS A 599 " --> pdb=" O TYR A 616 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR A 616 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS A 601 " --> pdb=" O ARG A 614 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A 612 " --> pdb=" O SER A 603 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 813 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: 1.10 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 669 1.32 - 1.44: 1283 1.44 - 1.57: 2474 1.57 - 1.69: 1 1.69 - 1.81: 52 Bond restraints: 4479 Sorted by residual: bond pdb=" CA LEU A 27 " pdb=" C LEU A 27 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.11e-02 8.12e+03 2.60e+01 bond pdb=" C SER A 630 " pdb=" O SER A 630 " ideal model delta sigma weight residual 1.237 1.196 0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" O22 FY5 A 801 " pdb=" S21 FY5 A 801 " ideal model delta sigma weight residual 1.461 1.527 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" O20 FY5 A 801 " pdb=" S21 FY5 A 801 " ideal model delta sigma weight residual 1.673 1.613 0.060 2.00e-02 2.50e+03 8.98e+00 bond pdb=" O23 FY5 A 801 " pdb=" S21 FY5 A 801 " ideal model delta sigma weight residual 1.458 1.399 0.059 2.00e-02 2.50e+03 8.70e+00 ... (remaining 4474 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 5686 2.18 - 4.36: 307 4.36 - 6.54: 44 6.54 - 8.72: 20 8.72 - 10.90: 16 Bond angle restraints: 6073 Sorted by residual: angle pdb=" N LYS A 28 " pdb=" CA LYS A 28 " pdb=" C LYS A 28 " ideal model delta sigma weight residual 113.41 103.39 10.02 1.22e+00 6.72e-01 6.74e+01 angle pdb=" N GLN A 369 " pdb=" CA GLN A 369 " pdb=" C GLN A 369 " ideal model delta sigma weight residual 109.64 118.36 -8.72 1.27e+00 6.20e-01 4.72e+01 angle pdb=" N GLU A 523 " pdb=" CA GLU A 523 " pdb=" C GLU A 523 " ideal model delta sigma weight residual 110.59 100.77 9.82 1.45e+00 4.76e-01 4.58e+01 angle pdb=" C PHE A 278 " pdb=" CA PHE A 278 " pdb=" CB PHE A 278 " ideal model delta sigma weight residual 111.51 101.08 10.43 1.58e+00 4.01e-01 4.36e+01 angle pdb=" N GLU A 60 " pdb=" CA GLU A 60 " pdb=" C GLU A 60 " ideal model delta sigma weight residual 111.52 120.47 -8.95 1.40e+00 5.10e-01 4.09e+01 ... (remaining 6068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.85: 2488 20.85 - 41.69: 154 41.69 - 62.54: 24 62.54 - 83.38: 1 83.38 - 104.23: 9 Dihedral angle restraints: 2676 sinusoidal: 1073 harmonic: 1603 Sorted by residual: dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -159.05 73.05 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS A 474 " pdb=" SG CYS A 474 " pdb=" SG CYS A 524 " pdb=" CB CYS A 524 " ideal model delta sinusoidal sigma weight residual 93.00 39.59 53.41 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" C CYS A 506 " pdb=" N CYS A 506 " pdb=" CA CYS A 506 " pdb=" CB CYS A 506 " ideal model delta harmonic sigma weight residual -122.60 -108.76 -13.84 0 2.50e+00 1.60e-01 3.07e+01 ... (remaining 2673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 668 0.126 - 0.252: 26 0.252 - 0.378: 7 0.378 - 0.504: 1 0.504 - 0.630: 3 Chirality restraints: 705 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 3.98e+01 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 516 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -3.03 0.63 2.00e-01 2.50e+01 9.93e+00 chirality pdb=" CA GLU A 60 " pdb=" N GLU A 60 " pdb=" C GLU A 60 " pdb=" CB GLU A 60 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.75e+00 ... (remaining 702 not shown) Planarity restraints: 737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.356 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG B 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.130 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.544 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 802 " 0.300 2.00e-02 2.50e+03 2.54e-01 8.06e+02 pdb=" C7 NAG A 802 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG A 802 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG A 802 " -0.438 2.00e-02 2.50e+03 pdb=" O7 NAG A 802 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.291 2.00e-02 2.50e+03 2.45e-01 7.53e+02 pdb=" C7 NAG B 2 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.420 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.022 2.00e-02 2.50e+03 ... (remaining 734 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1062 2.76 - 3.30: 4596 3.30 - 3.83: 7270 3.83 - 4.37: 8863 4.37 - 4.90: 14390 Nonbonded interactions: 36181 Sorted by model distance: nonbonded pdb=" O ILE A 595 " pdb=" OG1 THR A 598 " model vdw 2.231 3.040 nonbonded pdb=" NE2 GLN A 541 " pdb=" O23 FY5 A 801 " model vdw 2.370 3.120 nonbonded pdb=" O THR A 609 " pdb=" C ARG A 610 " model vdw 2.380 3.270 nonbonded pdb=" N GLU A 523 " pdb=" O GLU A 523 " model vdw 2.421 2.496 nonbonded pdb=" OD1 ASN A 432 " pdb=" OG1 THR A 619 " model vdw 2.423 3.040 ... (remaining 36176 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.480 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 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 : 0.008 0.066 4479 Z= 0.501 Angle : 1.221 10.896 6073 Z= 0.803 Chirality : 0.074 0.630 705 Planarity : 0.018 0.306 735 Dihedral : 14.366 104.227 1637 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.65 % Allowed : 5.17 % Favored : 94.18 % Cbeta Deviations : 0.79 % 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: -2.74 (0.30), residues: 552 helix: -0.97 (0.25), residues: 351 sheet: None (None), residues: 0 loop : -3.32 (0.32), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 259 HIS 0.006 0.002 HIS A 451 PHE 0.012 0.001 PHE A 117 TYR 0.019 0.001 TYR A 590 ARG 0.004 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 38 PHE cc_start: 0.6996 (m-80) cc_final: 0.6754 (m-80) REVERT: A 48 MET cc_start: 0.7698 (tpt) cc_final: 0.7447 (tpt) REVERT: A 86 TYR cc_start: 0.6727 (t80) cc_final: 0.6460 (t80) REVERT: A 568 LYS cc_start: 0.7704 (tttt) cc_final: 0.6777 (tptt) REVERT: A 640 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7549 (t80) outliers start: 3 outliers final: 0 residues processed: 100 average time/residue: 0.1533 time to fit residues: 19.6967 Evaluate side-chains 76 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 43 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 606 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4479 Z= 0.257 Angle : 0.723 13.600 6073 Z= 0.345 Chirality : 0.044 0.273 705 Planarity : 0.005 0.033 735 Dihedral : 8.654 74.091 706 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.23 % Allowed : 12.07 % Favored : 84.70 % 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: -0.44 (0.34), residues: 552 helix: 0.74 (0.26), residues: 359 sheet: None (None), residues: 0 loop : -2.31 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 259 HIS 0.004 0.001 HIS A 92 PHE 0.022 0.002 PHE A 341 TYR 0.018 0.002 TYR A 338 ARG 0.003 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 623 ARG cc_start: 0.7279 (ttt90) cc_final: 0.6326 (ttp-170) REVERT: A 640 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7657 (t80) REVERT: A 649 LYS cc_start: 0.7924 (tptt) cc_final: 0.6795 (mmtm) outliers start: 15 outliers final: 7 residues processed: 91 average time/residue: 0.1683 time to fit residues: 20.2233 Evaluate side-chains 79 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 4479 Z= 0.359 Angle : 0.687 13.791 6073 Z= 0.334 Chirality : 0.043 0.178 705 Planarity : 0.004 0.038 735 Dihedral : 7.237 74.608 706 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.31 % Allowed : 14.66 % Favored : 81.03 % 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: 0.04 (0.34), residues: 552 helix: 1.09 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -2.07 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 259 HIS 0.004 0.002 HIS A 115 PHE 0.020 0.002 PHE A 175 TYR 0.023 0.002 TYR A 590 ARG 0.003 0.001 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8587 (mtp) cc_final: 0.8114 (mtp) REVERT: A 623 ARG cc_start: 0.7507 (ttt90) cc_final: 0.6529 (ttp-170) REVERT: A 640 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7628 (t80) outliers start: 20 outliers final: 14 residues processed: 86 average time/residue: 0.1425 time to fit residues: 16.1150 Evaluate side-chains 87 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4479 Z= 0.233 Angle : 0.620 14.611 6073 Z= 0.297 Chirality : 0.040 0.157 705 Planarity : 0.004 0.038 735 Dihedral : 6.995 74.026 706 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.66 % Allowed : 17.24 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.35), residues: 552 helix: 1.33 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.71 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 259 HIS 0.003 0.001 HIS A 92 PHE 0.017 0.001 PHE A 175 TYR 0.019 0.002 TYR A 590 ARG 0.002 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7024 (mt) cc_final: 0.6821 (mp) REVERT: A 118 MET cc_start: 0.8610 (mtp) cc_final: 0.8093 (mtp) REVERT: A 517 TYR cc_start: 0.6130 (m-80) cc_final: 0.5449 (m-10) REVERT: A 623 ARG cc_start: 0.7488 (ttt90) cc_final: 0.6429 (ttp-170) REVERT: A 640 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7719 (t80) outliers start: 17 outliers final: 12 residues processed: 86 average time/residue: 0.1418 time to fit residues: 16.1744 Evaluate side-chains 80 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.0870 chunk 22 optimal weight: 0.0970 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4479 Z= 0.196 Angle : 0.582 12.579 6073 Z= 0.281 Chirality : 0.039 0.141 705 Planarity : 0.004 0.038 735 Dihedral : 6.868 72.316 706 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.37 % Allowed : 19.40 % Favored : 78.23 % 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: 0.85 (0.36), residues: 552 helix: 1.68 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -1.54 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 259 HIS 0.008 0.001 HIS A 575 PHE 0.017 0.001 PHE A 175 TYR 0.020 0.001 TYR A 590 ARG 0.002 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8583 (mtp) cc_final: 0.8286 (mtp) REVERT: A 217 MET cc_start: 0.8100 (mmt) cc_final: 0.7732 (mmt) REVERT: A 517 TYR cc_start: 0.6003 (m-80) cc_final: 0.5386 (m-10) REVERT: A 623 ARG cc_start: 0.7415 (ttt90) cc_final: 0.6481 (ttp-170) REVERT: A 640 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7724 (t80) outliers start: 11 outliers final: 7 residues processed: 87 average time/residue: 0.1423 time to fit residues: 16.5433 Evaluate side-chains 81 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 0.0170 chunk 39 optimal weight: 2.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4479 Z= 0.245 Angle : 0.573 7.281 6073 Z= 0.285 Chirality : 0.040 0.133 705 Planarity : 0.004 0.040 735 Dihedral : 6.931 71.563 706 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.09 % Allowed : 18.53 % Favored : 77.37 % 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: 0.89 (0.36), residues: 552 helix: 1.70 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.51 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 602 HIS 0.005 0.001 HIS A 575 PHE 0.017 0.001 PHE A 175 TYR 0.021 0.001 TYR A 590 ARG 0.002 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 TYR cc_start: 0.6132 (m-80) cc_final: 0.5570 (m-10) REVERT: A 623 ARG cc_start: 0.7421 (ttt90) cc_final: 0.6421 (ttt180) REVERT: A 640 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.7707 (t80) outliers start: 19 outliers final: 14 residues processed: 85 average time/residue: 0.1365 time to fit residues: 15.7038 Evaluate side-chains 84 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.0470 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 4479 Z= 0.215 Angle : 0.554 7.195 6073 Z= 0.278 Chirality : 0.039 0.131 705 Planarity : 0.004 0.038 735 Dihedral : 6.936 70.349 706 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.02 % Allowed : 19.40 % Favored : 77.59 % 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: 1.05 (0.36), residues: 552 helix: 1.79 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -1.40 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 259 HIS 0.004 0.001 HIS A 575 PHE 0.017 0.001 PHE A 175 TYR 0.022 0.001 TYR A 442 ARG 0.002 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 TYR cc_start: 0.6125 (m-80) cc_final: 0.5590 (m-10) REVERT: A 557 MET cc_start: 0.8023 (ttm) cc_final: 0.7737 (mtp) REVERT: A 623 ARG cc_start: 0.7463 (ttt90) cc_final: 0.6464 (ttt180) REVERT: A 640 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7695 (t80) outliers start: 14 outliers final: 13 residues processed: 82 average time/residue: 0.1339 time to fit residues: 14.7676 Evaluate side-chains 83 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.0970 chunk 42 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 4479 Z= 0.204 Angle : 0.542 6.985 6073 Z= 0.276 Chirality : 0.039 0.130 705 Planarity : 0.003 0.038 735 Dihedral : 6.955 69.301 706 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.66 % Allowed : 19.61 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.21 (0.36), residues: 552 helix: 1.89 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -1.27 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 259 HIS 0.004 0.001 HIS A 575 PHE 0.017 0.001 PHE A 175 TYR 0.020 0.001 TYR A 590 ARG 0.002 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ILE cc_start: 0.8475 (tp) cc_final: 0.8194 (tt) REVERT: A 517 TYR cc_start: 0.6102 (m-80) cc_final: 0.5592 (m-10) REVERT: A 557 MET cc_start: 0.8043 (ttm) cc_final: 0.7774 (mtp) REVERT: A 623 ARG cc_start: 0.7480 (ttt90) cc_final: 0.6446 (ttt180) REVERT: A 640 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7675 (t80) outliers start: 17 outliers final: 15 residues processed: 83 average time/residue: 0.1360 time to fit residues: 15.2392 Evaluate side-chains 89 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 4479 Z= 0.247 Angle : 0.562 6.854 6073 Z= 0.288 Chirality : 0.040 0.142 705 Planarity : 0.004 0.037 735 Dihedral : 6.999 68.974 706 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.53 % Allowed : 19.18 % Favored : 76.29 % 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: 1.23 (0.36), residues: 552 helix: 1.88 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -1.20 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 602 HIS 0.003 0.001 HIS A 115 PHE 0.017 0.001 PHE A 175 TYR 0.020 0.001 TYR A 590 ARG 0.002 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 TYR cc_start: 0.8069 (m-80) cc_final: 0.7862 (m-80) REVERT: A 517 TYR cc_start: 0.6171 (m-80) cc_final: 0.5661 (m-10) REVERT: A 623 ARG cc_start: 0.7470 (ttt90) cc_final: 0.6447 (ttt180) REVERT: A 640 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.7689 (t80) outliers start: 21 outliers final: 16 residues processed: 85 average time/residue: 0.1271 time to fit residues: 14.7615 Evaluate side-chains 87 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.0040 chunk 35 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4479 Z= 0.203 Angle : 0.542 6.903 6073 Z= 0.279 Chirality : 0.039 0.143 705 Planarity : 0.004 0.037 735 Dihedral : 6.942 67.831 706 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.45 % Allowed : 20.26 % Favored : 76.29 % 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: 1.35 (0.36), residues: 552 helix: 1.94 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -1.10 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 259 HIS 0.003 0.001 HIS A 575 PHE 0.016 0.001 PHE A 175 TYR 0.019 0.001 TYR A 590 ARG 0.002 0.000 ARG A 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 TYR cc_start: 0.6130 (m-80) cc_final: 0.5652 (m-10) REVERT: A 623 ARG cc_start: 0.7472 (ttt90) cc_final: 0.6464 (ttt180) REVERT: A 640 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7657 (t80) outliers start: 16 outliers final: 13 residues processed: 85 average time/residue: 0.1486 time to fit residues: 16.6060 Evaluate side-chains 84 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.177201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132509 restraints weight = 4757.674| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.14 r_work: 0.3205 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4479 Z= 0.210 Angle : 0.545 6.946 6073 Z= 0.281 Chirality : 0.039 0.148 705 Planarity : 0.004 0.037 735 Dihedral : 6.936 67.268 706 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.45 % Allowed : 20.04 % Favored : 76.51 % 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: 1.39 (0.36), residues: 552 helix: 1.96 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -1.03 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 259 HIS 0.003 0.001 HIS A 575 PHE 0.024 0.001 PHE A 73 TYR 0.019 0.001 TYR A 590 ARG 0.006 0.001 ARG A 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1260.26 seconds wall clock time: 23 minutes 43.70 seconds (1423.70 seconds total)