Starting phenix.real_space_refine (version: dev) on Fri May 13 11:26:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5o_23678/05_2022/7m5o_23678.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5o_23678/05_2022/7m5o_23678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5o_23678/05_2022/7m5o_23678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5o_23678/05_2022/7m5o_23678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5o_23678/05_2022/7m5o_23678.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5o_23678/05_2022/7m5o_23678.pdb" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.173 sd= 0.984 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 11648 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 10449 Classifications: {'peptide': 655} Link IDs: {'PTRANS': 39, 'TRANS': 615} Chain breaks: 1 Chain: "B" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1198 Classifications: {'RNA': 37} Modifications used: {'rna3p_pyr': 11, 'rna2p_pur': 7, 'rna3p_pur': 15, 'rna2p_pyr': 4} Link IDs: {'rna3p': 26, 'rna2p': 10} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9735 SG CYS A 667 47.731 13.611 37.310 1.00139.12 S ATOM 9782 SG CYS A 670 48.241 12.976 33.639 1.00137.51 S ATOM 9984 SG CYS A 685 44.845 12.824 35.611 1.00142.82 S ATOM 10024 SG CYS A 688 47.103 9.939 35.540 1.00139.82 S Time building chain proxies: 5.74, per 1000 atoms: 0.49 Number of scatterers: 11648 At special positions: 0 Unit cell: (79.165, 88.085, 111.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 20 16.00 P 37 15.00 O 1218 8.00 N 1104 7.00 C 3633 6.00 H 5635 1.00 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: 8.89 Conformation dependent library (CDL) restraints added in 967.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 688 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 670 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 685 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 667 " Number of angles added : 6 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 3 sheets defined 45.8% alpha, 8.7% beta 5 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 4.93 Creating SS restraints... Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.582A pdb=" N ALA A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 100 removed outlier: 3.912A pdb=" N ARG A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 129 through 169 removed outlier: 3.999A pdb=" N LEU A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.650A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 removed outlier: 3.930A pdb=" N ASP A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.994A pdb=" N ARG A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 373 through 383 removed outlier: 4.085A pdb=" N ALA A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.658A pdb=" N GLN A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLU A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 Processing helix chain 'A' and resid 499 through 509 removed outlier: 3.613A pdb=" N GLU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 549 through 567 removed outlier: 3.965A pdb=" N LEU A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 597 removed outlier: 3.930A pdb=" N LEU A 571 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 removed outlier: 3.602A pdb=" N PHE A 626 " --> pdb=" O TRP A 623 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A 627 " --> pdb=" O ASP A 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 623 through 627' Processing helix chain 'A' and resid 635 through 651 removed outlier: 4.174A pdb=" N THR A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 664 removed outlier: 4.612A pdb=" N THR A 663 " --> pdb=" O ARG A 659 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER A 664 " --> pdb=" O PRO A 660 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 659 through 664' Processing helix chain 'A' and resid 674 through 678 removed outlier: 4.245A pdb=" N ARG A 678 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 709 removed outlier: 3.863A pdb=" N THR A 709 " --> pdb=" O GLN A 705 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 199 removed outlier: 5.543A pdb=" N VAL A 66 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASP A 312 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 68 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 304 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 262 Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 371 removed outlier: 6.656A pdb=" N LEU A 370 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 658 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL A 604 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 391 " --> pdb=" O VAL A 604 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N GLU A 606 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N ILE A 393 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG A 407 " --> pdb=" O PRO A 419 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 9.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 5623 1.04 - 1.23: 113 1.23 - 1.43: 2616 1.43 - 1.63: 3478 1.63 - 1.82: 25 Bond restraints: 11855 Sorted by residual: bond pdb=" CA PRO A 191 " pdb=" C PRO A 191 " ideal model delta sigma weight residual 1.517 1.523 -0.006 6.70e-03 2.23e+04 8.64e-01 bond pdb=" CB LYS A 669 " pdb=" CG LYS A 669 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.57e-01 bond pdb=" CB CYS A 685 " pdb=" HB3 CYS A 685 " ideal model delta sigma weight residual 0.970 0.987 -0.017 2.00e-02 2.50e+03 7.04e-01 bond pdb=" N ILE A 232 " pdb=" CA ILE A 232 " ideal model delta sigma weight residual 1.468 1.458 0.010 1.22e-02 6.72e+03 6.55e-01 bond pdb=" CB TRP A 287 " pdb=" CG TRP A 287 " ideal model delta sigma weight residual 1.498 1.473 0.025 3.10e-02 1.04e+03 6.39e-01 ... (remaining 11850 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.10: 496 107.10 - 113.85: 13789 113.85 - 120.59: 4143 120.59 - 127.33: 2840 127.33 - 134.07: 152 Bond angle restraints: 21420 Sorted by residual: angle pdb=" CA CYS A 685 " pdb=" CB CYS A 685 " pdb=" SG CYS A 685 " ideal model delta sigma weight residual 114.40 109.44 4.96 2.30e+00 1.89e-01 4.65e+00 angle pdb=" N ASP A 421 " pdb=" CA ASP A 421 " pdb=" C ASP A 421 " ideal model delta sigma weight residual 108.13 111.72 -3.59 1.72e+00 3.38e-01 4.36e+00 angle pdb=" CA GLU A 632 " pdb=" CB GLU A 632 " pdb=" CG GLU A 632 " ideal model delta sigma weight residual 114.10 118.03 -3.93 2.00e+00 2.50e-01 3.87e+00 angle pdb=" N GLU A 411 " pdb=" CA GLU A 411 " pdb=" C GLU A 411 " ideal model delta sigma weight residual 109.50 106.54 2.96 1.58e+00 4.01e-01 3.52e+00 angle pdb=" N THR A 409 " pdb=" CA THR A 409 " pdb=" C THR A 409 " ideal model delta sigma weight residual 110.80 106.89 3.91 2.13e+00 2.20e-01 3.37e+00 ... (remaining 21415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.17: 4517 26.17 - 52.35: 186 52.35 - 78.52: 35 78.52 - 104.69: 9 104.69 - 130.86: 3 Dihedral angle restraints: 4750 sinusoidal: 2551 harmonic: 2199 Sorted by residual: dihedral pdb=" CA PRO A 660 " pdb=" C PRO A 660 " pdb=" N GLU A 661 " pdb=" CA GLU A 661 " ideal model delta harmonic sigma weight residual -180.00 -148.91 -31.09 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA ASP A 421 " pdb=" C ASP A 421 " pdb=" N ARG A 422 " pdb=" CA ARG A 422 " ideal model delta harmonic sigma weight residual 180.00 154.54 25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" O4' A B 8 " pdb=" C1' A B 8 " pdb=" N9 A B 8 " pdb=" C4 A B 8 " ideal model delta sinusoidal sigma weight residual -106.00 -178.61 72.61 1 1.70e+01 3.46e-03 2.33e+01 ... (remaining 4747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 589 0.025 - 0.050: 259 0.050 - 0.075: 69 0.075 - 0.100: 32 0.100 - 0.124: 31 Chirality restraints: 980 Sorted by residual: chirality pdb=" CA ILE A 351 " pdb=" N ILE A 351 " pdb=" C ILE A 351 " pdb=" CB ILE A 351 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 232 " pdb=" N ILE A 232 " pdb=" C ILE A 232 " pdb=" CB ILE A 232 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE A 325 " pdb=" N ILE A 325 " pdb=" C ILE A 325 " pdb=" CB ILE A 325 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 977 not shown) Planarity restraints: 1623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 455 " 0.039 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO A 456 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 276 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 277 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 667 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO A 668 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 668 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 668 " 0.022 5.00e-02 4.00e+02 ... (remaining 1620 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 492 2.16 - 2.77: 21747 2.77 - 3.38: 31525 3.38 - 3.99: 38662 3.99 - 4.60: 58960 Nonbonded interactions: 151386 Sorted by model distance: nonbonded pdb=" O SER A 105 " pdb=" HD1 HIS A 109 " model vdw 1.545 1.850 nonbonded pdb="HH21 ARG A 212 " pdb=" OE2 GLU A 214 " model vdw 1.593 1.850 nonbonded pdb=" HE ARG A 226 " pdb=" O ALA A 297 " model vdw 1.598 1.850 nonbonded pdb=" OD1 ASN A 497 " pdb=" HZ1 LYS A 536 " model vdw 1.605 1.850 nonbonded pdb="HD21 ASN A 586 " pdb=" OP1 A B -1 " model vdw 1.612 1.850 ... (remaining 151381 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 37 5.49 5 S 20 5.16 5 C 3633 2.51 5 N 1104 2.21 5 O 1218 1.98 5 H 5635 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.180 Extract box with map and model: 2.760 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 44.880 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 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 : 0.003 0.028 6220 Z= 0.189 Angle : 0.545 4.959 8611 Z= 0.310 Chirality : 0.036 0.124 980 Planarity : 0.004 0.059 978 Dihedral : 15.947 130.863 2467 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.31), residues: 651 helix: -0.30 (0.32), residues: 257 sheet: -1.90 (0.53), residues: 87 loop : -2.07 (0.32), residues: 307 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 140 average time/residue: 0.3606 time to fit residues: 67.3029 Evaluate side-chains 111 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 0.918 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1649 time to fit residues: 2.0184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 6220 Z= 0.200 Angle : 0.587 5.026 8611 Z= 0.312 Chirality : 0.038 0.134 980 Planarity : 0.005 0.062 978 Dihedral : 13.307 130.528 1169 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 1.25 % 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: -1.10 (0.32), residues: 651 helix: 0.62 (0.32), residues: 261 sheet: -1.17 (0.53), residues: 87 loop : -1.81 (0.33), residues: 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 120 average time/residue: 0.3251 time to fit residues: 52.5254 Evaluate side-chains 117 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.935 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.2021 time to fit residues: 2.9763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 46 optimal weight: 0.0020 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 6220 Z= 0.248 Angle : 0.592 6.808 8611 Z= 0.314 Chirality : 0.038 0.151 980 Planarity : 0.005 0.070 978 Dihedral : 13.398 132.289 1169 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 2.14 % 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: -0.70 (0.32), residues: 651 helix: 0.95 (0.31), residues: 266 sheet: -0.70 (0.65), residues: 70 loop : -1.69 (0.33), residues: 315 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 119 average time/residue: 0.3334 time to fit residues: 53.5155 Evaluate side-chains 117 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.806 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1970 time to fit residues: 3.5425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 chunk 37 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 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 151 ASN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 6220 Z= 0.167 Angle : 0.559 6.621 8611 Z= 0.291 Chirality : 0.037 0.126 980 Planarity : 0.005 0.051 978 Dihedral : 13.262 130.627 1169 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 1.60 % 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: -0.26 (0.33), residues: 651 helix: 1.41 (0.32), residues: 265 sheet: -0.69 (0.64), residues: 70 loop : -1.48 (0.34), residues: 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 120 average time/residue: 0.3398 time to fit residues: 55.0771 Evaluate side-chains 114 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 0.906 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1508 time to fit residues: 2.4132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 6220 Z= 0.209 Angle : 0.567 8.066 8611 Z= 0.295 Chirality : 0.037 0.136 980 Planarity : 0.005 0.072 978 Dihedral : 13.260 131.042 1169 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.33), residues: 651 helix: 1.60 (0.32), residues: 265 sheet: -0.78 (0.63), residues: 68 loop : -1.50 (0.34), residues: 318 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 119 average time/residue: 0.3542 time to fit residues: 56.4386 Evaluate side-chains 115 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 0.920 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.2183 time to fit residues: 4.0226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 6220 Z= 0.171 Angle : 0.544 6.208 8611 Z= 0.281 Chirality : 0.037 0.127 980 Planarity : 0.004 0.044 978 Dihedral : 13.168 129.941 1169 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 1.78 % 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: 0.01 (0.34), residues: 651 helix: 1.82 (0.33), residues: 264 sheet: -0.73 (0.63), residues: 68 loop : -1.45 (0.34), residues: 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 122 average time/residue: 0.3379 time to fit residues: 55.6064 Evaluate side-chains 114 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.932 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.2110 time to fit residues: 2.9820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.0670 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 6220 Z= 0.220 Angle : 0.572 8.215 8611 Z= 0.297 Chirality : 0.038 0.124 980 Planarity : 0.005 0.037 978 Dihedral : 13.210 130.569 1169 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 1.60 % 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: -0.07 (0.34), residues: 651 helix: 1.80 (0.33), residues: 264 sheet: -1.23 (0.57), residues: 76 loop : -1.42 (0.35), residues: 311 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 119 average time/residue: 0.3690 time to fit residues: 57.9641 Evaluate side-chains 118 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.967 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.2116 time to fit residues: 3.6570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 0.0870 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 62 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 6220 Z= 0.158 Angle : 0.551 7.679 8611 Z= 0.284 Chirality : 0.037 0.129 980 Planarity : 0.005 0.040 978 Dihedral : 13.064 128.493 1169 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 1.07 % 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: 0.15 (0.34), residues: 651 helix: 1.96 (0.33), residues: 264 sheet: -1.14 (0.57), residues: 78 loop : -1.26 (0.35), residues: 309 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 117 average time/residue: 0.3548 time to fit residues: 55.2212 Evaluate side-chains 118 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 0.920 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.2456 time to fit residues: 2.8510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 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 162 ASN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.092 6220 Z= 0.179 Angle : 0.549 7.910 8611 Z= 0.283 Chirality : 0.037 0.126 980 Planarity : 0.005 0.042 978 Dihedral : 13.026 128.831 1169 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 1.25 % 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: 0.27 (0.34), residues: 651 helix: 2.04 (0.33), residues: 265 sheet: -1.05 (0.56), residues: 78 loop : -1.19 (0.35), residues: 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 119 average time/residue: 0.3614 time to fit residues: 57.0066 Evaluate side-chains 117 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 0.944 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.2692 time to fit residues: 2.6914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 3.9990 chunk 62 optimal weight: 0.0270 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0170 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.090 6220 Z= 0.194 Angle : 0.545 7.785 8611 Z= 0.282 Chirality : 0.036 0.126 980 Planarity : 0.005 0.086 978 Dihedral : 12.959 128.098 1169 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.71 % 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: 0.37 (0.34), residues: 651 helix: 2.10 (0.33), residues: 265 sheet: -0.94 (0.56), residues: 78 loop : -1.13 (0.35), residues: 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 119 average time/residue: 0.3561 time to fit residues: 56.7638 Evaluate side-chains 114 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 0.904 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.2900 time to fit residues: 2.3226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.101470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085554 restraints weight = 42617.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.089006 restraints weight = 15547.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.090996 restraints weight = 7643.112| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.120 6220 Z= 0.168 Angle : 0.552 8.164 8611 Z= 0.286 Chirality : 0.037 0.174 980 Planarity : 0.006 0.081 978 Dihedral : 12.920 127.689 1169 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 0.89 % 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: 0.30 (0.34), residues: 651 helix: 2.17 (0.33), residues: 265 sheet: -1.28 (0.51), residues: 92 loop : -1.18 (0.36), residues: 294 =============================================================================== Job complete usr+sys time: 3180.21 seconds wall clock time: 56 minutes 52.05 seconds (3412.05 seconds total)