Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 18:15:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psm_13614/10_2023/7psm_13614_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psm_13614/10_2023/7psm_13614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psm_13614/10_2023/7psm_13614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psm_13614/10_2023/7psm_13614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psm_13614/10_2023/7psm_13614_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psm_13614/10_2023/7psm_13614_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 6038 2.51 5 N 1602 2.21 5 O 1710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A GLU 528": "OE1" <-> "OE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B GLU 598": "OE1" <-> "OE2" Residue "B GLU 608": "OE1" <-> "OE2" Residue "B GLU 658": "OE1" <-> "OE2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B GLU 675": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 9394 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4622 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 17, 'TRANS': 567} Chain: "B" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4622 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 17, 'TRANS': 567} Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 5.60, per 1000 atoms: 0.60 Number of scatterers: 9394 At special positions: 0 Unit cell: (82.467, 77.469, 141.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 8 15.00 Mg 2 11.99 O 1710 8.00 N 1602 7.00 C 6038 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: 3.75 Conformation dependent library (CDL) restraints added in 1.4 seconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 4 sheets defined 61.0% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 105 through 139 Proline residue: A 129 - end of helix removed outlier: 3.598A pdb=" N MET A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 199 removed outlier: 3.996A pdb=" N THR A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 211 through 234 Processing helix chain 'A' and resid 236 through 253 Processing helix chain 'A' and resid 257 through 303 removed outlier: 5.370A pdb=" N HIS A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N PHE A 283 " --> pdb=" O TRP A 279 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 314 through 366 removed outlier: 4.052A pdb=" N SER A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 395 Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 575 through 589 Processing helix chain 'A' and resid 605 through 616 Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 666 through 675 Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 105 through 139 Proline residue: B 129 - end of helix removed outlier: 3.593A pdb=" N MET B 139 " --> pdb=" O THR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 199 removed outlier: 4.022A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 211 through 234 Processing helix chain 'B' and resid 236 through 253 Processing helix chain 'B' and resid 257 through 303 removed outlier: 5.371A pdb=" N HIS B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE B 283 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 284 " --> pdb=" O ARG B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 314 through 366 removed outlier: 4.052A pdb=" N SER B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 395 Proline residue: B 388 - end of helix Processing helix chain 'B' and resid 400 through 413 Processing helix chain 'B' and resid 476 through 482 Processing helix chain 'B' and resid 505 through 509 Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 539 through 548 Processing helix chain 'B' and resid 552 through 557 Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 575 through 589 Processing helix chain 'B' and resid 605 through 616 Processing helix chain 'B' and resid 656 through 660 Processing helix chain 'B' and resid 666 through 675 Processing sheet with id= A, first strand: chain 'A' and resid 457 through 459 Processing sheet with id= B, first strand: chain 'A' and resid 641 through 645 Processing sheet with id= C, first strand: chain 'B' and resid 457 through 459 Processing sheet with id= D, first strand: chain 'B' and resid 641 through 645 552 hydrogen bonds defined for protein. 1638 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: 2.64 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 1496 1.29 - 1.42: 2402 1.42 - 1.55: 5589 1.55 - 1.68: 13 1.68 - 1.81: 68 Bond restraints: 9568 Sorted by residual: bond pdb=" C3' ANP B 701 " pdb=" C4' ANP B 701 " ideal model delta sigma weight residual 1.532 1.308 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C3' ANP A 701 " pdb=" C4' ANP A 701 " ideal model delta sigma weight residual 1.532 1.309 0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C4' ANP A 701 " pdb=" O4' ANP A 701 " ideal model delta sigma weight residual 1.431 1.623 -0.192 2.00e-02 2.50e+03 9.21e+01 bond pdb=" C4' ANP B 701 " pdb=" O4' ANP B 701 " ideal model delta sigma weight residual 1.431 1.623 -0.192 2.00e-02 2.50e+03 9.19e+01 bond pdb=" C6 ANP B 701 " pdb=" N6 ANP B 701 " ideal model delta sigma weight residual 1.340 1.474 -0.134 2.00e-02 2.50e+03 4.51e+01 ... (remaining 9563 not shown) Histogram of bond angle deviations from ideal: 99.24 - 107.22: 253 107.22 - 115.20: 5881 115.20 - 123.17: 6442 123.17 - 131.15: 328 131.15 - 139.13: 38 Bond angle restraints: 12942 Sorted by residual: angle pdb=" C1' ANP A 701 " pdb=" N9 ANP A 701 " pdb=" C4 ANP A 701 " ideal model delta sigma weight residual 125.38 111.09 14.29 3.00e+00 1.11e-01 2.27e+01 angle pdb=" C1' ANP B 701 " pdb=" N9 ANP B 701 " pdb=" C4 ANP B 701 " ideal model delta sigma weight residual 125.38 111.10 14.28 3.00e+00 1.11e-01 2.27e+01 angle pdb=" O3 LOP A 703 " pdb=" P1 LOP A 703 " pdb=" O4 LOP A 703 " ideal model delta sigma weight residual 120.67 108.32 12.35 3.00e+00 1.11e-01 1.69e+01 angle pdb=" O3 LOP B 703 " pdb=" P1 LOP B 703 " pdb=" O4 LOP B 703 " ideal model delta sigma weight residual 120.67 108.34 12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C ARG B 188 " pdb=" CA ARG B 188 " pdb=" CB ARG B 188 " ideal model delta sigma weight residual 110.88 104.55 6.33 1.57e+00 4.06e-01 1.63e+01 ... (remaining 12937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.22: 5393 26.22 - 52.44: 280 52.44 - 78.66: 39 78.66 - 104.89: 0 104.89 - 131.11: 2 Dihedral angle restraints: 5714 sinusoidal: 2330 harmonic: 3384 Sorted by residual: dihedral pdb=" O1A ANP A 701 " pdb=" O3A ANP A 701 " pdb=" PA ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sinusoidal sigma weight residual 83.11 -48.00 131.11 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" O1A ANP B 701 " pdb=" O3A ANP B 701 " pdb=" PA ANP B 701 " pdb=" PB ANP B 701 " ideal model delta sinusoidal sigma weight residual 83.11 -47.95 131.06 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C VAL B 128 " pdb=" N VAL B 128 " pdb=" CA VAL B 128 " pdb=" CB VAL B 128 " ideal model delta harmonic sigma weight residual -122.00 -131.14 9.14 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 5711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1127 0.054 - 0.109: 300 0.109 - 0.163: 57 0.163 - 0.217: 6 0.217 - 0.272: 4 Chirality restraints: 1494 Sorted by residual: chirality pdb=" CB ILE B 419 " pdb=" CA ILE B 419 " pdb=" CG1 ILE B 419 " pdb=" CG2 ILE B 419 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE A 419 " pdb=" CA ILE A 419 " pdb=" CG1 ILE A 419 " pdb=" CG2 ILE A 419 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB VAL B 128 " pdb=" CA VAL B 128 " pdb=" CG1 VAL B 128 " pdb=" CG2 VAL B 128 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1491 not shown) Planarity restraints: 1616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 594 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C MET B 594 " 0.034 2.00e-02 2.50e+03 pdb=" O MET B 594 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE B 595 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 594 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C MET A 594 " -0.034 2.00e-02 2.50e+03 pdb=" O MET A 594 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE A 595 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 376 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C VAL A 376 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL A 376 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU A 377 " 0.011 2.00e-02 2.50e+03 ... (remaining 1613 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 104 2.64 - 3.21: 8257 3.21 - 3.77: 14720 3.77 - 4.34: 19064 4.34 - 4.90: 32115 Nonbonded interactions: 74260 Sorted by model distance: nonbonded pdb=" O2B ANP A 701 " pdb="MG MG A 702 " model vdw 2.078 2.170 nonbonded pdb=" O2B ANP B 701 " pdb="MG MG B 702 " model vdw 2.079 2.170 nonbonded pdb=" O3G ANP A 701 " pdb="MG MG A 702 " model vdw 2.093 2.170 nonbonded pdb=" O3G ANP B 701 " pdb="MG MG B 702 " model vdw 2.095 2.170 nonbonded pdb=" OE1 GLN B 517 " pdb="MG MG B 702 " model vdw 2.117 2.170 ... (remaining 74255 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.95 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.700 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.410 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 0.224 9568 Z= 0.475 Angle : 1.044 14.289 12942 Z= 0.511 Chirality : 0.052 0.272 1494 Planarity : 0.006 0.045 1616 Dihedral : 15.591 131.107 3530 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % 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: -3.29 (0.20), residues: 1166 helix: -1.52 (0.14), residues: 788 sheet: -3.68 (0.43), residues: 82 loop : -3.03 (0.31), residues: 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.168 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2849 time to fit residues: 68.7038 Evaluate side-chains 133 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.3980 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN B 127 GLN ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9568 Z= 0.163 Angle : 0.499 6.883 12942 Z= 0.263 Chirality : 0.038 0.136 1494 Planarity : 0.004 0.030 1616 Dihedral : 10.093 156.398 1332 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.70 % Allowed : 15.07 % Favored : 83.23 % 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: -0.81 (0.24), residues: 1166 helix: 0.54 (0.18), residues: 788 sheet: -2.40 (0.62), residues: 48 loop : -2.88 (0.30), residues: 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 0.947 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 166 average time/residue: 0.2479 time to fit residues: 56.4758 Evaluate side-chains 152 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0845 time to fit residues: 3.7029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 9568 Z= 0.396 Angle : 0.628 6.981 12942 Z= 0.325 Chirality : 0.043 0.146 1494 Planarity : 0.004 0.032 1616 Dihedral : 9.270 139.189 1332 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.30 % Allowed : 18.56 % Favored : 79.14 % 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 (0.25), residues: 1166 helix: 0.93 (0.18), residues: 782 sheet: -2.45 (0.62), residues: 48 loop : -2.92 (0.31), residues: 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 160 average time/residue: 0.2172 time to fit residues: 48.5784 Evaluate side-chains 146 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0893 time to fit residues: 3.7446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 ASN B 235 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9568 Z= 0.180 Angle : 0.494 6.846 12942 Z= 0.260 Chirality : 0.039 0.139 1494 Planarity : 0.003 0.031 1616 Dihedral : 8.946 139.202 1332 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.90 % Allowed : 20.66 % Favored : 77.45 % 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: 0.22 (0.25), residues: 1166 helix: 1.47 (0.19), residues: 780 sheet: -2.30 (0.64), residues: 48 loop : -2.75 (0.31), residues: 338 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 155 average time/residue: 0.2284 time to fit residues: 48.9890 Evaluate side-chains 145 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0899 time to fit residues: 3.0051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 100 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS A 347 ASN B 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9568 Z= 0.176 Angle : 0.501 6.696 12942 Z= 0.261 Chirality : 0.039 0.137 1494 Planarity : 0.003 0.029 1616 Dihedral : 8.646 134.431 1332 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.40 % Allowed : 21.36 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1166 helix: 1.75 (0.19), residues: 776 sheet: -2.06 (0.66), residues: 48 loop : -2.59 (0.31), residues: 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 1.179 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 163 average time/residue: 0.2224 time to fit residues: 50.8329 Evaluate side-chains 143 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0881 time to fit residues: 2.8338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.0980 chunk 112 optimal weight: 6.9990 chunk 93 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.7728 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9568 Z= 0.213 Angle : 0.527 9.463 12942 Z= 0.274 Chirality : 0.040 0.138 1494 Planarity : 0.003 0.029 1616 Dihedral : 8.377 131.345 1332 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.40 % Allowed : 21.96 % Favored : 76.65 % 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: 0.69 (0.25), residues: 1166 helix: 1.80 (0.19), residues: 776 sheet: -1.87 (0.68), residues: 48 loop : -2.48 (0.31), residues: 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 1.124 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 143 average time/residue: 0.2280 time to fit residues: 45.7367 Evaluate side-chains 141 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1098 time to fit residues: 3.8547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.7750 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9568 Z= 0.256 Angle : 0.544 9.150 12942 Z= 0.282 Chirality : 0.041 0.139 1494 Planarity : 0.003 0.029 1616 Dihedral : 8.084 129.574 1332 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.50 % Allowed : 21.86 % Favored : 76.65 % 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: 0.82 (0.25), residues: 1166 helix: 1.89 (0.19), residues: 762 sheet: -1.80 (0.68), residues: 48 loop : -2.22 (0.31), residues: 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.139 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 148 average time/residue: 0.2243 time to fit residues: 46.3077 Evaluate side-chains 138 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0877 time to fit residues: 2.8423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7705 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9568 Z= 0.176 Angle : 0.506 8.917 12942 Z= 0.263 Chirality : 0.039 0.149 1494 Planarity : 0.003 0.029 1616 Dihedral : 7.722 128.569 1332 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.70 % Allowed : 22.46 % Favored : 76.85 % 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: 1.08 (0.25), residues: 1166 helix: 2.07 (0.19), residues: 762 sheet: -1.64 (0.69), residues: 48 loop : -2.08 (0.31), residues: 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 1.063 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 140 average time/residue: 0.2227 time to fit residues: 43.7980 Evaluate side-chains 136 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0892 time to fit residues: 2.3846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 0.0570 chunk 67 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9568 Z= 0.170 Angle : 0.535 12.068 12942 Z= 0.272 Chirality : 0.039 0.135 1494 Planarity : 0.003 0.029 1616 Dihedral : 7.413 125.497 1332 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.30 % Allowed : 23.45 % Favored : 76.25 % 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: 1.22 (0.25), residues: 1166 helix: 2.16 (0.19), residues: 762 sheet: -1.52 (0.71), residues: 48 loop : -1.97 (0.32), residues: 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 139 time to evaluate : 1.097 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 139 average time/residue: 0.2566 time to fit residues: 49.5747 Evaluate side-chains 128 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1121 time to fit residues: 2.3994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7696 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9568 Z= 0.189 Angle : 0.540 11.607 12942 Z= 0.276 Chirality : 0.039 0.152 1494 Planarity : 0.003 0.032 1616 Dihedral : 7.255 123.342 1332 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.30 % Allowed : 23.45 % Favored : 76.25 % 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: 1.25 (0.25), residues: 1166 helix: 2.16 (0.19), residues: 762 sheet: -1.48 (0.73), residues: 48 loop : -1.90 (0.32), residues: 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 1.079 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 130 average time/residue: 0.2279 time to fit residues: 41.4638 Evaluate side-chains 129 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0896 time to fit residues: 2.0178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 0.0570 chunk 66 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.130434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107651 restraints weight = 12645.915| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.58 r_work: 0.3175 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9568 Z= 0.179 Angle : 0.541 11.990 12942 Z= 0.275 Chirality : 0.039 0.149 1494 Planarity : 0.003 0.031 1616 Dihedral : 7.160 122.043 1332 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.20 % Allowed : 23.65 % Favored : 76.15 % 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: 1.31 (0.26), residues: 1166 helix: 2.18 (0.19), residues: 762 sheet: -1.39 (0.74), residues: 48 loop : -1.83 (0.32), residues: 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2001.65 seconds wall clock time: 37 minutes 5.04 seconds (2225.04 seconds total)