Starting phenix.real_space_refine on Sun Mar 10 15:33:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/03_2024/7n5f_24188_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/03_2024/7n5f_24188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/03_2024/7n5f_24188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/03_2024/7n5f_24188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/03_2024/7n5f_24188_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/03_2024/7n5f_24188_updated.pdb" } resolution = 2.7 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= 0.001 sd= 0.027 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 12 5.16 5 C 1996 2.51 5 N 503 2.21 5 O 526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3037 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3037 Unusual residues: {'PLM': 1} Classifications: {'peptide': 386, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 378, None: 1} Not linked: pdbres="ASN A 751 " pdbres="PLM A 801 " Chain breaks: 5 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Time building chain proxies: 2.29, per 1000 atoms: 0.75 Number of scatterers: 3037 At special positions: 0 Unit cell: (56.65, 90.64, 141.11, 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 12 16.00 O 526 8.00 N 503 7.00 C 1996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.3 seconds 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 2 sheets defined 61.9% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 191 through 201 Processing helix chain 'A' and resid 223 through 243 removed outlier: 4.233A pdb=" N LEU A 226 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU A 234 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 282 removed outlier: 5.237A pdb=" N THR A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 332 removed outlier: 4.266A pdb=" N HIS A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 352 Processing helix chain 'A' and resid 504 through 551 Processing helix chain 'A' and resid 557 through 573 removed outlier: 3.585A pdb=" N PHE A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 589 Processing helix chain 'A' and resid 631 through 636 removed outlier: 4.907A pdb=" N THR A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 678 Processing helix chain 'A' and resid 715 through 736 Processing sheet with id= A, first strand: chain 'A' and resid 639 through 641 removed outlier: 6.640A pdb=" N VAL A 618 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N MET A 612 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N THR A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 649 through 657 removed outlier: 6.783A pdb=" N ALA A 703 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL A 691 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE A 705 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N MET A 689 " --> pdb=" O PHE A 705 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASN A 707 " --> pdb=" O HIS A 687 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N HIS A 687 " --> pdb=" O ASN A 707 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 579 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: 0.85 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 566 1.31 - 1.44: 824 1.44 - 1.56: 1667 1.56 - 1.69: 16 1.69 - 1.82: 21 Bond restraints: 3094 Sorted by residual: bond pdb=" CB HIS A 331 " pdb=" CG HIS A 331 " ideal model delta sigma weight residual 1.497 1.404 0.093 1.40e-02 5.10e+03 4.39e+01 bond pdb=" CB ILE A 285 " pdb=" CG1 ILE A 285 " ideal model delta sigma weight residual 1.530 1.654 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" NE1 TRP A 273 " pdb=" CE2 TRP A 273 " ideal model delta sigma weight residual 1.370 1.315 0.055 1.10e-02 8.26e+03 2.52e+01 bond pdb=" CB LEU A 258 " pdb=" CG LEU A 258 " ideal model delta sigma weight residual 1.530 1.628 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" CB TYR A 629 " pdb=" CG TYR A 629 " ideal model delta sigma weight residual 1.512 1.406 0.106 2.20e-02 2.07e+03 2.34e+01 ... (remaining 3089 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.20: 63 106.20 - 113.17: 1680 113.17 - 120.13: 1293 120.13 - 127.10: 1120 127.10 - 134.07: 34 Bond angle restraints: 4190 Sorted by residual: angle pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " pdb=" CG PHE A 335 " ideal model delta sigma weight residual 113.80 122.07 -8.27 1.00e+00 1.00e+00 6.83e+01 angle pdb=" C LEU A 743 " pdb=" N PRO A 744 " pdb=" CA PRO A 744 " ideal model delta sigma weight residual 119.85 126.24 -6.39 1.01e+00 9.80e-01 4.00e+01 angle pdb=" C HIS A 592 " pdb=" N PRO A 593 " pdb=" CA PRO A 593 " ideal model delta sigma weight residual 119.56 125.29 -5.73 1.01e+00 9.80e-01 3.22e+01 angle pdb=" C SER A 645 " pdb=" N PRO A 646 " pdb=" CA PRO A 646 " ideal model delta sigma weight residual 120.98 126.89 -5.91 1.07e+00 8.73e-01 3.05e+01 angle pdb=" C TYR A 629 " pdb=" N PRO A 630 " pdb=" CA PRO A 630 " ideal model delta sigma weight residual 119.76 125.32 -5.56 1.03e+00 9.43e-01 2.91e+01 ... (remaining 4185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 1782 17.70 - 35.40: 36 35.40 - 53.09: 8 53.09 - 70.79: 2 70.79 - 88.49: 3 Dihedral angle restraints: 1831 sinusoidal: 699 harmonic: 1132 Sorted by residual: dihedral pdb=" N PHE A 335 " pdb=" C PHE A 335 " pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " ideal model delta harmonic sigma weight residual 122.80 130.99 -8.19 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" N ARG A 296 " pdb=" C ARG A 296 " pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " ideal model delta harmonic sigma weight residual 122.80 114.65 8.15 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CB GLU A 611 " pdb=" CG GLU A 611 " pdb=" CD GLU A 611 " pdb=" OE1 GLU A 611 " ideal model delta sinusoidal sigma weight residual 0.00 -88.49 88.49 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 1828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 408 0.108 - 0.216: 84 0.216 - 0.323: 12 0.323 - 0.431: 0 0.431 - 0.539: 2 Chirality restraints: 506 Sorted by residual: chirality pdb=" CB ILE A 285 " pdb=" CA ILE A 285 " pdb=" CG1 ILE A 285 " pdb=" CG2 ILE A 285 " both_signs ideal model delta sigma weight residual False 2.64 3.18 -0.54 2.00e-01 2.50e+01 7.25e+00 chirality pdb=" CG LEU A 258 " pdb=" CB LEU A 258 " pdb=" CD1 LEU A 258 " pdb=" CD2 LEU A 258 " both_signs ideal model delta sigma weight residual False -2.59 -3.12 0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" CA PHE A 335 " pdb=" N PHE A 335 " pdb=" C PHE A 335 " pdb=" CB PHE A 335 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 503 not shown) Planarity restraints: 511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 335 " -0.059 2.00e-02 2.50e+03 3.66e-02 2.35e+01 pdb=" CG PHE A 335 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE A 335 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 335 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE A 335 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 335 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 335 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 697 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C VAL A 697 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL A 697 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 698 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 329 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C SER A 329 " 0.051 2.00e-02 2.50e+03 pdb=" O SER A 329 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE A 330 " -0.017 2.00e-02 2.50e+03 ... (remaining 508 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.95: 1545 2.95 - 3.44: 3145 3.44 - 3.93: 4812 3.93 - 4.41: 5632 4.41 - 4.90: 8454 Nonbonded interactions: 23588 Sorted by model distance: nonbonded pdb=" N ASN A 711 " pdb=" O ASN A 711 " model vdw 2.468 2.496 nonbonded pdb=" NZ LYS A 730 " pdb=" OE2 GLU A 734 " model vdw 2.473 2.520 nonbonded pdb=" N VAL A 697 " pdb=" N ASN A 698 " model vdw 2.491 2.560 nonbonded pdb=" NZ LYS A 579 " pdb=" OE2 GLU A 583 " model vdw 2.506 2.520 nonbonded pdb=" N THR A 295 " pdb=" N ARG A 296 " model vdw 2.536 2.560 ... (remaining 23583 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: 0.920 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: 4.420 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.480 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:11.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 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 : 0.023 0.124 3094 Z= 1.462 Angle : 1.502 8.265 4190 Z= 1.032 Chirality : 0.097 0.539 506 Planarity : 0.008 0.037 511 Dihedral : 9.991 88.488 1085 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 0.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 1.68 (0.40), residues: 374 helix: 1.43 (0.29), residues: 242 sheet: 0.14 (0.80), residues: 38 loop : 1.02 (0.67), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.007 TRP A 622 HIS 0.009 0.003 HIS A 331 PHE 0.059 0.006 PHE A 335 TYR 0.026 0.006 TYR A 675 ARG 0.007 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.370 Fit side-chains REVERT: A 350 GLN cc_start: 0.7950 (mt0) cc_final: 0.7715 (mt0) REVERT: A 548 TRP cc_start: 0.8678 (t60) cc_final: 0.8248 (t60) REVERT: A 591 MET cc_start: 0.7817 (mtp) cc_final: 0.7553 (mtp) REVERT: A 624 LYS cc_start: 0.8810 (mmtp) cc_final: 0.7292 (tmmt) REVERT: A 655 SER cc_start: 0.8107 (p) cc_final: 0.7870 (m) REVERT: A 675 TYR cc_start: 0.8227 (t80) cc_final: 0.7937 (t80) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.9567 time to fit residues: 149.7141 Evaluate side-chains 133 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 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 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN A 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3094 Z= 0.202 Angle : 0.548 6.051 4190 Z= 0.306 Chirality : 0.041 0.135 506 Planarity : 0.004 0.026 511 Dihedral : 5.895 48.608 411 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 4.13 % Allowed : 18.10 % Favored : 77.78 % 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: 3.29 (0.45), residues: 374 helix: 2.91 (0.32), residues: 232 sheet: 0.70 (0.76), residues: 44 loop : 1.19 (0.79), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 507 HIS 0.007 0.002 HIS A 331 PHE 0.016 0.002 PHE A 335 TYR 0.005 0.001 TYR A 628 ARG 0.003 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.353 Fit side-chains REVERT: A 261 THR cc_start: 0.7097 (m) cc_final: 0.6815 (p) REVERT: A 300 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7837 (mp0) REVERT: A 319 LYS cc_start: 0.7839 (tmmt) cc_final: 0.7621 (ttpt) REVERT: A 350 GLN cc_start: 0.7793 (mt0) cc_final: 0.7515 (mt0) REVERT: A 624 LYS cc_start: 0.8704 (mmtp) cc_final: 0.7110 (tmmt) REVERT: A 626 LYS cc_start: 0.5896 (OUTLIER) cc_final: 0.4336 (mptp) REVERT: A 655 SER cc_start: 0.8117 (p) cc_final: 0.7868 (m) outliers start: 13 outliers final: 3 residues processed: 128 average time/residue: 0.9043 time to fit residues: 119.4519 Evaluate side-chains 125 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 632 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN A 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3094 Z= 0.190 Angle : 0.480 6.428 4190 Z= 0.268 Chirality : 0.041 0.141 506 Planarity : 0.003 0.023 511 Dihedral : 5.542 46.741 411 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 7.30 % Allowed : 21.27 % Favored : 71.43 % 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: 2.98 (0.44), residues: 374 helix: 2.79 (0.32), residues: 232 sheet: 0.43 (0.72), residues: 44 loop : 0.76 (0.76), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 507 HIS 0.005 0.002 HIS A 592 PHE 0.027 0.002 PHE A 344 TYR 0.012 0.001 TYR A 675 ARG 0.003 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 0.364 Fit side-chains REVERT: A 271 PHE cc_start: 0.7874 (t80) cc_final: 0.7615 (t80) REVERT: A 300 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7769 (mp0) REVERT: A 624 LYS cc_start: 0.8711 (mmtp) cc_final: 0.7142 (tmmt) REVERT: A 626 LYS cc_start: 0.5811 (OUTLIER) cc_final: 0.4341 (mptp) REVERT: A 655 SER cc_start: 0.8120 (p) cc_final: 0.7885 (m) outliers start: 23 outliers final: 8 residues processed: 128 average time/residue: 0.8848 time to fit residues: 116.7231 Evaluate side-chains 129 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 748 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 HIS A 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3094 Z= 0.186 Angle : 0.467 6.876 4190 Z= 0.259 Chirality : 0.041 0.153 506 Planarity : 0.003 0.020 511 Dihedral : 5.466 44.608 411 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 5.08 % Allowed : 25.71 % Favored : 69.21 % 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: 2.62 (0.44), residues: 374 helix: 2.57 (0.33), residues: 238 sheet: 0.23 (0.76), residues: 42 loop : 0.33 (0.72), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 507 HIS 0.005 0.002 HIS A 592 PHE 0.009 0.001 PHE A 301 TYR 0.017 0.001 TYR A 675 ARG 0.002 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.353 Fit side-chains REVERT: A 271 PHE cc_start: 0.7898 (t80) cc_final: 0.7634 (t80) REVERT: A 350 GLN cc_start: 0.7735 (mt0) cc_final: 0.7448 (mt0) REVERT: A 535 LEU cc_start: 0.8774 (tm) cc_final: 0.8535 (tp) REVERT: A 624 LYS cc_start: 0.8709 (mmtp) cc_final: 0.7153 (tmmt) REVERT: A 626 LYS cc_start: 0.5837 (OUTLIER) cc_final: 0.4339 (mptp) outliers start: 16 outliers final: 6 residues processed: 124 average time/residue: 0.9353 time to fit residues: 119.4339 Evaluate side-chains 125 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 724 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.0170 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3094 Z= 0.256 Angle : 0.484 5.048 4190 Z= 0.269 Chirality : 0.041 0.163 506 Planarity : 0.003 0.021 511 Dihedral : 5.541 43.303 411 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 6.67 % Allowed : 24.76 % Favored : 68.57 % 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: 2.63 (0.44), residues: 374 helix: 2.59 (0.33), residues: 232 sheet: 0.55 (0.73), residues: 44 loop : 0.30 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 683 HIS 0.005 0.001 HIS A 592 PHE 0.013 0.002 PHE A 260 TYR 0.020 0.002 TYR A 675 ARG 0.004 0.001 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 0.366 Fit side-chains REVERT: A 350 GLN cc_start: 0.7740 (mt0) cc_final: 0.7459 (mt0) REVERT: A 576 ASN cc_start: 0.7072 (t0) cc_final: 0.6772 (t0) REVERT: A 582 PHE cc_start: 0.7950 (t80) cc_final: 0.7707 (t80) REVERT: A 624 LYS cc_start: 0.8709 (mmtp) cc_final: 0.7165 (tmmt) REVERT: A 626 LYS cc_start: 0.5875 (OUTLIER) cc_final: 0.4361 (mptp) outliers start: 21 outliers final: 11 residues processed: 126 average time/residue: 0.9692 time to fit residues: 125.7165 Evaluate side-chains 128 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 748 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.0170 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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: 0.7185 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3094 Z= 0.144 Angle : 0.457 7.229 4190 Z= 0.248 Chirality : 0.040 0.159 506 Planarity : 0.002 0.020 511 Dihedral : 5.227 40.322 411 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.44 % Allowed : 27.62 % Favored : 67.94 % 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: 2.53 (0.44), residues: 374 helix: 2.52 (0.33), residues: 238 sheet: 0.28 (0.75), residues: 42 loop : 0.17 (0.73), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 304 HIS 0.004 0.001 HIS A 592 PHE 0.007 0.001 PHE A 336 TYR 0.016 0.001 TYR A 675 ARG 0.002 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 0.331 Fit side-chains REVERT: A 350 GLN cc_start: 0.7721 (mt0) cc_final: 0.7440 (mt0) REVERT: A 535 LEU cc_start: 0.8761 (tm) cc_final: 0.8503 (tp) REVERT: A 576 ASN cc_start: 0.7038 (t0) cc_final: 0.6756 (t0) REVERT: A 582 PHE cc_start: 0.7859 (t80) cc_final: 0.7528 (t80) REVERT: A 624 LYS cc_start: 0.8697 (mmtp) cc_final: 0.7233 (tmmt) REVERT: A 671 ARG cc_start: 0.7708 (mmm-85) cc_final: 0.7469 (mmm160) outliers start: 14 outliers final: 6 residues processed: 121 average time/residue: 0.9939 time to fit residues: 123.8148 Evaluate side-chains 124 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 748 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 0.0670 chunk 23 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3094 Z= 0.144 Angle : 0.445 5.908 4190 Z= 0.242 Chirality : 0.039 0.168 506 Planarity : 0.002 0.020 511 Dihedral : 5.036 39.166 411 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.76 % Allowed : 27.94 % Favored : 67.30 % 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: 2.69 (0.45), residues: 374 helix: 2.72 (0.33), residues: 237 sheet: -0.07 (0.72), residues: 47 loop : 0.28 (0.78), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 507 HIS 0.004 0.001 HIS A 592 PHE 0.016 0.001 PHE A 260 TYR 0.013 0.001 TYR A 675 ARG 0.002 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 0.340 Fit side-chains REVERT: A 350 GLN cc_start: 0.7859 (mt0) cc_final: 0.7585 (mt0) REVERT: A 535 LEU cc_start: 0.8773 (tm) cc_final: 0.8548 (tp) REVERT: A 582 PHE cc_start: 0.7852 (t80) cc_final: 0.7512 (t80) REVERT: A 624 LYS cc_start: 0.8699 (mmtp) cc_final: 0.7248 (tmmt) outliers start: 15 outliers final: 8 residues processed: 122 average time/residue: 0.9500 time to fit residues: 119.3711 Evaluate side-chains 128 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 734 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 26 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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: 0.7169 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3094 Z= 0.133 Angle : 0.445 6.308 4190 Z= 0.243 Chirality : 0.040 0.166 506 Planarity : 0.002 0.020 511 Dihedral : 4.909 38.840 411 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.17 % Allowed : 30.16 % Favored : 66.67 % 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: 2.66 (0.45), residues: 374 helix: 2.70 (0.33), residues: 237 sheet: -0.05 (0.73), residues: 47 loop : 0.23 (0.78), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 507 HIS 0.003 0.001 HIS A 592 PHE 0.006 0.001 PHE A 336 TYR 0.011 0.001 TYR A 675 ARG 0.003 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 0.378 Fit side-chains REVERT: A 350 GLN cc_start: 0.7823 (mt0) cc_final: 0.7552 (mt0) REVERT: A 582 PHE cc_start: 0.7851 (t80) cc_final: 0.7512 (t80) REVERT: A 624 LYS cc_start: 0.8727 (mmtp) cc_final: 0.7266 (tmmt) outliers start: 10 outliers final: 4 residues processed: 124 average time/residue: 0.9318 time to fit residues: 118.9867 Evaluate side-chains 124 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 692 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3094 Z= 0.164 Angle : 0.467 7.379 4190 Z= 0.253 Chirality : 0.040 0.172 506 Planarity : 0.002 0.020 511 Dihedral : 4.879 40.532 411 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.86 % Allowed : 29.84 % Favored : 67.30 % 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: 2.56 (0.45), residues: 374 helix: 2.61 (0.33), residues: 237 sheet: -0.08 (0.73), residues: 47 loop : 0.25 (0.78), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 316 HIS 0.004 0.001 HIS A 592 PHE 0.015 0.001 PHE A 260 TYR 0.029 0.002 TYR A 675 ARG 0.002 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.368 Fit side-chains REVERT: A 350 GLN cc_start: 0.7828 (mt0) cc_final: 0.7562 (mt0) REVERT: A 535 LEU cc_start: 0.8774 (tm) cc_final: 0.8528 (tp) REVERT: A 582 PHE cc_start: 0.7911 (t80) cc_final: 0.7584 (t80) REVERT: A 624 LYS cc_start: 0.8724 (mmtp) cc_final: 0.7264 (tmmt) REVERT: A 671 ARG cc_start: 0.7762 (mmm-85) cc_final: 0.7518 (mmm160) outliers start: 9 outliers final: 5 residues processed: 124 average time/residue: 0.9886 time to fit residues: 126.1915 Evaluate side-chains 126 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 689 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 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 648 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3094 Z= 0.182 Angle : 0.487 7.320 4190 Z= 0.269 Chirality : 0.041 0.175 506 Planarity : 0.003 0.022 511 Dihedral : 4.858 40.763 411 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.22 % Allowed : 31.43 % Favored : 66.35 % 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: 2.45 (0.46), residues: 374 helix: 2.51 (0.33), residues: 237 sheet: -0.05 (0.73), residues: 47 loop : 0.19 (0.79), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 316 HIS 0.004 0.001 HIS A 592 PHE 0.007 0.001 PHE A 301 TYR 0.028 0.002 TYR A 675 ARG 0.002 0.000 ARG A 296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.371 Fit side-chains REVERT: A 350 GLN cc_start: 0.7719 (mt0) cc_final: 0.7433 (mt0) REVERT: A 535 LEU cc_start: 0.8763 (tm) cc_final: 0.8490 (tp) REVERT: A 582 PHE cc_start: 0.7915 (t80) cc_final: 0.7581 (t80) REVERT: A 624 LYS cc_start: 0.8716 (mmtp) cc_final: 0.7257 (tmmt) REVERT: A 671 ARG cc_start: 0.7771 (mmm-85) cc_final: 0.7524 (mmm160) outliers start: 7 outliers final: 5 residues processed: 118 average time/residue: 0.9987 time to fit residues: 121.2773 Evaluate side-chains 122 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 689 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.0370 chunk 0 optimal weight: 5.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.155287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.138421 restraints weight = 4525.773| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.04 r_work: 0.3805 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3094 Z= 0.158 Angle : 0.486 7.211 4190 Z= 0.267 Chirality : 0.040 0.171 506 Planarity : 0.003 0.022 511 Dihedral : 4.791 39.803 411 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.90 % Allowed : 31.43 % Favored : 66.67 % 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: 2.54 (0.45), residues: 374 helix: 2.52 (0.33), residues: 237 sheet: 0.60 (0.80), residues: 37 loop : 0.10 (0.74), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 316 HIS 0.003 0.001 HIS A 592 PHE 0.016 0.001 PHE A 260 TYR 0.028 0.002 TYR A 675 ARG 0.002 0.000 ARG A 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2336.38 seconds wall clock time: 41 minutes 46.16 seconds (2506.16 seconds total)