Sun 23 Dec 23:55:22 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ii1-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ii1-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ii1-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-4.0-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-4.0-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 23:55:26 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-4.0-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 727 and 0 Target number of residues in the AU: 727 Target solvent content: 0.6456 Checking the provided sequence file Detected sequence length: 301 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1204 Adjusted target solvent content: 0.41 Input MTZ file: 2ii1-4.0-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 1 Cell parameters: 43.759 69.605 94.984 73.954 88.905 86.625 Input sequence file: 2ii1-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 9632 target number of atoms Had to go as low as 0.65 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 91.283 4.000 Wilson plot Bfac: 75.38 8241 reflections ( 91.02 % complete ) and 0 restraints for refining 10600 atoms. Observations/parameters ratio is 0.19 ------------------------------------------------------ Starting model: R = 0.3360 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3235 (Rfree = 0.000) for 10600 atoms. Found 50 (50 requested) and removed 256 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 4.03 Search for helices and strands: 0 residues in 0 chains, 10507 seeds are put forward NCS extension: 0 residues added, 10507 seeds are put forward Round 1: 219 peptides, 50 chains. Longest chain 7 peptides. Score 0.206 Round 2: 294 peptides, 62 chains. Longest chain 8 peptides. Score 0.252 Round 3: 313 peptides, 61 chains. Longest chain 9 peptides. Score 0.292 Round 4: 314 peptides, 58 chains. Longest chain 10 peptides. Score 0.315 Round 5: 338 peptides, 66 chains. Longest chain 9 peptides. Score 0.298 Taking the results from Round 4 Chains 58, Residues 256, Estimated correctness of the model 0.0 % 6 chains (34 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 21693 restraints for refining 8695 atoms. 20649 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2745 (Rfree = 0.000) for 8695 atoms. Found 41 (41 requested) and removed 81 (20 requested) atoms. Cycle 2: After refmac, R = 0.2591 (Rfree = 0.000) for 8564 atoms. Found 41 (41 requested) and removed 77 (20 requested) atoms. Cycle 3: After refmac, R = 0.2532 (Rfree = 0.000) for 8468 atoms. Found 40 (40 requested) and removed 64 (20 requested) atoms. Cycle 4: After refmac, R = 0.1938 (Rfree = 0.000) for 8402 atoms. Found 19 (40 requested) and removed 50 (20 requested) atoms. Cycle 5: After refmac, R = 0.1714 (Rfree = 0.000) for 8345 atoms. Found 13 (39 requested) and removed 33 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 4.02 Search for helices and strands: 0 residues in 0 chains, 8492 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 8502 seeds are put forward Round 1: 267 peptides, 63 chains. Longest chain 6 peptides. Score 0.195 Round 2: 319 peptides, 63 chains. Longest chain 11 peptides. Score 0.288 Round 3: 347 peptides, 67 chains. Longest chain 13 peptides. Score 0.306 Round 4: 374 peptides, 69 chains. Longest chain 10 peptides. Score 0.335 Round 5: 354 peptides, 65 chains. Longest chain 12 peptides. Score 0.331 Taking the results from Round 4 Chains 69, Residues 305, Estimated correctness of the model 0.0 % 7 chains (35 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 18777 restraints for refining 7897 atoms. 17558 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2154 (Rfree = 0.000) for 7897 atoms. Found 37 (37 requested) and removed 70 (18 requested) atoms. Cycle 7: After refmac, R = 0.2042 (Rfree = 0.000) for 7810 atoms. Found 37 (37 requested) and removed 67 (18 requested) atoms. Cycle 8: After refmac, R = 0.1897 (Rfree = 0.000) for 7759 atoms. Found 36 (36 requested) and removed 75 (18 requested) atoms. Cycle 9: After refmac, R = 0.1830 (Rfree = 0.000) for 7701 atoms. Found 36 (36 requested) and removed 52 (18 requested) atoms. Cycle 10: After refmac, R = 0.1746 (Rfree = 0.000) for 7679 atoms. Found 36 (36 requested) and removed 33 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 4.01 Search for helices and strands: 0 residues in 0 chains, 7877 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 7888 seeds are put forward Round 1: 343 peptides, 74 chains. Longest chain 8 peptides. Score 0.250 Round 2: 380 peptides, 71 chains. Longest chain 13 peptides. Score 0.331 Round 3: 382 peptides, 64 chains. Longest chain 14 peptides. Score 0.381 Round 4: 380 peptides, 64 chains. Longest chain 16 peptides. Score 0.378 Round 5: 412 peptides, 74 chains. Longest chain 16 peptides. Score 0.361 Taking the results from Round 3 Chains 65, Residues 318, Estimated correctness of the model 0.0 % 8 chains (38 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 19224 restraints for refining 8073 atoms. 17933 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1837 (Rfree = 0.000) for 8073 atoms. Found 28 (38 requested) and removed 67 (19 requested) atoms. Cycle 12: After refmac, R = 0.1822 (Rfree = 0.000) for 8003 atoms. Found 38 (38 requested) and removed 48 (19 requested) atoms. Cycle 13: After refmac, R = 0.1858 (Rfree = 0.000) for 7977 atoms. Found 37 (37 requested) and removed 40 (18 requested) atoms. Cycle 14: After refmac, R = 0.1742 (Rfree = 0.000) for 7956 atoms. Found 37 (37 requested) and removed 38 (18 requested) atoms. Cycle 15: After refmac, R = 0.1337 (Rfree = 0.000) for 7948 atoms. Found 8 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 4.00 Search for helices and strands: 0 residues in 0 chains, 8156 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 8170 seeds are put forward Round 1: 309 peptides, 67 chains. Longest chain 10 peptides. Score 0.242 Round 2: 367 peptides, 67 chains. Longest chain 13 peptides. Score 0.338 Round 3: 388 peptides, 67 chains. Longest chain 14 peptides. Score 0.370 Round 4: 388 peptides, 65 chains. Longest chain 16 peptides. Score 0.384 Round 5: 380 peptides, 65 chains. Longest chain 12 peptides. Score 0.371 Taking the results from Round 4 Chains 68, Residues 323, Estimated correctness of the model 0.0 % 12 chains (70 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 19647 restraints for refining 8339 atoms. 18239 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1789 (Rfree = 0.000) for 8339 atoms. Found 39 (39 requested) and removed 80 (19 requested) atoms. Cycle 17: After refmac, R = 0.1710 (Rfree = 0.000) for 8251 atoms. Found 39 (39 requested) and removed 43 (19 requested) atoms. Cycle 18: After refmac, R = 0.1596 (Rfree = 0.000) for 8230 atoms. Found 35 (39 requested) and removed 52 (19 requested) atoms. Cycle 19: After refmac, R = 0.1548 (Rfree = 0.000) for 8204 atoms. Found 39 (39 requested) and removed 47 (19 requested) atoms. Cycle 20: After refmac, R = 0.1474 (Rfree = 0.000) for 8187 atoms. Found 38 (38 requested) and removed 37 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 4.01 Search for helices and strands: 0 residues in 0 chains, 8403 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 8420 seeds are put forward Round 1: 341 peptides, 70 chains. Longest chain 12 peptides. Score 0.275 Round 2: 356 peptides, 69 chains. Longest chain 10 peptides. Score 0.307 Round 3: 355 peptides, 68 chains. Longest chain 9 peptides. Score 0.312 Round 4: 352 peptides, 66 chains. Longest chain 13 peptides. Score 0.321 Round 5: 367 peptides, 69 chains. Longest chain 10 peptides. Score 0.324 Taking the results from Round 5 Chains 69, Residues 298, Estimated correctness of the model 0.0 % 10 chains (44 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 20849 restraints for refining 8581 atoms. 19633 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1802 (Rfree = 0.000) for 8581 atoms. Found 40 (40 requested) and removed 93 (20 requested) atoms. Cycle 22: After refmac, R = 0.1806 (Rfree = 0.000) for 8490 atoms. Found 40 (40 requested) and removed 50 (20 requested) atoms. Cycle 23: After refmac, R = 0.1691 (Rfree = 0.000) for 8453 atoms. Found 40 (40 requested) and removed 60 (20 requested) atoms. Cycle 24: After refmac, R = 0.1331 (Rfree = 0.000) for 8422 atoms. Found 14 (40 requested) and removed 30 (20 requested) atoms. Cycle 25: After refmac, R = 0.1255 (Rfree = 0.000) for 8393 atoms. Found 8 (39 requested) and removed 27 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 4.00 Search for helices and strands: 0 residues in 0 chains, 8578 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 8590 seeds are put forward Round 1: 285 peptides, 64 chains. Longest chain 6 peptides. Score 0.221 Round 2: 325 peptides, 63 chains. Longest chain 13 peptides. Score 0.298 Round 3: 327 peptides, 63 chains. Longest chain 9 peptides. Score 0.301 Round 4: 311 peptides, 59 chains. Longest chain 9 peptides. Score 0.303 Round 5: 315 peptides, 59 chains. Longest chain 12 peptides. Score 0.310 Taking the results from Round 5 Chains 59, Residues 256, Estimated correctness of the model 0.0 % 7 chains (32 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 21483 restraints for refining 8608 atoms. 20458 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1726 (Rfree = 0.000) for 8608 atoms. Found 40 (40 requested) and removed 86 (20 requested) atoms. Cycle 27: After refmac, R = 0.1770 (Rfree = 0.000) for 8533 atoms. Found 40 (40 requested) and removed 70 (20 requested) atoms. Cycle 28: After refmac, R = 0.1676 (Rfree = 0.000) for 8487 atoms. Found 40 (40 requested) and removed 45 (20 requested) atoms. Cycle 29: After refmac, R = 0.1333 (Rfree = 0.000) for 8462 atoms. Found 24 (40 requested) and removed 29 (20 requested) atoms. Cycle 30: After refmac, R = 0.1220 (Rfree = 0.000) for 8447 atoms. Found 10 (40 requested) and removed 26 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 4.01 Search for helices and strands: 0 residues in 0 chains, 8600 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 8617 seeds are put forward Round 1: 277 peptides, 62 chains. Longest chain 8 peptides. Score 0.222 Round 2: 324 peptides, 63 chains. Longest chain 10 peptides. Score 0.296 Round 3: 325 peptides, 61 chains. Longest chain 12 peptides. Score 0.312 Round 4: 332 peptides, 61 chains. Longest chain 11 peptides. Score 0.323 Round 5: 340 peptides, 61 chains. Longest chain 13 peptides. Score 0.336 Taking the results from Round 5 Chains 61, Residues 279, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 21516 restraints for refining 8698 atoms. 20407 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1665 (Rfree = 0.000) for 8698 atoms. Found 40 (41 requested) and removed 73 (20 requested) atoms. Cycle 32: After refmac, R = 0.1605 (Rfree = 0.000) for 8632 atoms. Found 41 (41 requested) and removed 55 (20 requested) atoms. Cycle 33: After refmac, R = 0.1570 (Rfree = 0.000) for 8603 atoms. Found 40 (40 requested) and removed 47 (20 requested) atoms. Cycle 34: After refmac, R = 0.1522 (Rfree = 0.000) for 8578 atoms. Found 40 (40 requested) and removed 38 (20 requested) atoms. Cycle 35: After refmac, R = 0.1592 (Rfree = 0.000) for 8569 atoms. Found 40 (40 requested) and removed 40 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.95 Search for helices and strands: 0 residues in 0 chains, 8738 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 8755 seeds are put forward Round 1: 256 peptides, 57 chains. Longest chain 9 peptides. Score 0.221 Round 2: 292 peptides, 51 chains. Longest chain 12 peptides. Score 0.329 Round 3: 279 peptides, 50 chains. Longest chain 13 peptides. Score 0.315 Round 4: 291 peptides, 51 chains. Longest chain 12 peptides. Score 0.328 Round 5: 297 peptides, 55 chains. Longest chain 10 peptides. Score 0.309 Taking the results from Round 2 Chains 51, Residues 241, Estimated correctness of the model 0.0 % 5 chains (22 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 21622 restraints for refining 8697 atoms. 20668 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1655 (Rfree = 0.000) for 8697 atoms. Found 41 (41 requested) and removed 61 (20 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1533 (Rfree = 0.000) for 8663 atoms. Found 41 (41 requested) and removed 47 (20 requested) atoms. Cycle 38: After refmac, R = 0.1069 (Rfree = 0.000) for 8640 atoms. Found 12 (41 requested) and removed 34 (20 requested) atoms. Cycle 39: After refmac, R = 0.1009 (Rfree = 0.000) for 8611 atoms. Found 1 (40 requested) and removed 24 (20 requested) atoms. Cycle 40: After refmac, R = 0.1001 (Rfree = 0.000) for 8585 atoms. Found 4 (40 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 3.94 Search for helices and strands: 0 residues in 0 chains, 8741 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 8757 seeds are put forward Round 1: 257 peptides, 59 chains. Longest chain 8 peptides. Score 0.207 Round 2: 281 peptides, 58 chains. Longest chain 10 peptides. Score 0.259 Round 3: 279 peptides, 56 chains. Longest chain 10 peptides. Score 0.270 Round 4: 290 peptides, 58 chains. Longest chain 11 peptides. Score 0.275 Round 5: 286 peptides, 58 chains. Longest chain 11 peptides. Score 0.268 Taking the results from Round 4 Chains 58, Residues 232, Estimated correctness of the model 0.0 % 6 chains (20 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 21860 restraints for refining 8697 atoms. 20951 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1525 (Rfree = 0.000) for 8697 atoms. Found 41 (41 requested) and removed 34 (20 requested) atoms. Cycle 42: After refmac, R = 0.1519 (Rfree = 0.000) for 8685 atoms. Found 41 (41 requested) and removed 37 (20 requested) atoms. Cycle 43: After refmac, R = 0.1038 (Rfree = 0.000) for 8674 atoms. Found 15 (41 requested) and removed 24 (20 requested) atoms. Cycle 44: After refmac, R = 0.0959 (Rfree = 0.000) for 8660 atoms. Found 7 (41 requested) and removed 25 (20 requested) atoms. Cycle 45: After refmac, R = 0.0917 (Rfree = 0.000) for 8637 atoms. Found 8 (41 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.95 Search for helices and strands: 0 residues in 0 chains, 8778 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8793 seeds are put forward Round 1: 255 peptides, 59 chains. Longest chain 7 peptides. Score 0.204 Round 2: 272 peptides, 55 chains. Longest chain 9 peptides. Score 0.265 Round 3: 264 peptides, 51 chains. Longest chain 13 peptides. Score 0.282 Round 4: 253 peptides, 49 chains. Longest chain 12 peptides. Score 0.277 Round 5: 251 peptides, 46 chains. Longest chain 13 peptides. Score 0.297 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 46, Residues 205, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2ii1-4_warpNtrace.pdb as input Building loops using Loopy2018 46 chains (205 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8241 reflections ( 91.02 % complete ) and 22196 restraints for refining 8697 atoms. 21396 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1525 (Rfree = 0.000) for 8697 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.1505 (Rfree = 0.000) for 8655 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.1042 (Rfree = 0.000) for 8619 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.0929 (Rfree = 0.000) for 8583 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Writing output files ... TimeTaking 78.67