null Mon 24 Dec 00:49:31 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 2iiu-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2iiu-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2iiu-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.2-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/2iiu-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.2-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 ============================================================ Mon 24 Dec 00:49:35 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/2iiu-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.2-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 543 and 0 Target number of residues in the AU: 543 Target solvent content: 0.6149 Checking the provided sequence file Detected sequence length: 227 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 681 Adjusted target solvent content: 0.52 Input MTZ file: 2iiu-3.2-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: 155 Cell parameters: 99.900 99.900 397.311 90.000 90.000 120.000 Input sequence file: 2iiu-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5448 target number of atoms Had to go as low as 0.75 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: 132.437 3.200 Wilson plot Bfac: 58.76 12997 reflections ( 99.27 % complete ) and 0 restraints for refining 6078 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3348 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2673 (Rfree = 0.000) for 6078 atoms. Found 44 (54 requested) and removed 65 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 2.97 Search for helices and strands: 0 residues in 0 chains, 6222 seeds are put forward NCS extension: 0 residues added, 6222 seeds are put forward Round 1: 319 peptides, 60 chains. Longest chain 15 peptides. Score 0.354 Round 2: 393 peptides, 60 chains. Longest chain 34 peptides. Score 0.502 Round 3: 426 peptides, 63 chains. Longest chain 20 peptides. Score 0.538 Round 4: 416 peptides, 58 chains. Longest chain 18 peptides. Score 0.558 Round 5: 431 peptides, 58 chains. Longest chain 25 peptides. Score 0.583 Taking the results from Round 5 Chains 59, Residues 373, Estimated correctness of the model 36.4 % 2 chains (39 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 10379 restraints for refining 4973 atoms. 8786 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2685 (Rfree = 0.000) for 4973 atoms. Found 44 (44 requested) and removed 38 (22 requested) atoms. Cycle 2: After refmac, R = 0.2499 (Rfree = 0.000) for 4928 atoms. Found 20 (44 requested) and removed 29 (22 requested) atoms. Cycle 3: After refmac, R = 0.2454 (Rfree = 0.000) for 4891 atoms. Found 21 (44 requested) and removed 28 (22 requested) atoms. Cycle 4: After refmac, R = 0.2442 (Rfree = 0.000) for 4873 atoms. Found 17 (43 requested) and removed 21 (21 requested) atoms. Cycle 5: After refmac, R = 0.2409 (Rfree = 0.000) for 4856 atoms. Found 22 (43 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.07 2.99 Search for helices and strands: 0 residues in 0 chains, 5068 seeds are put forward NCS extension: 0 residues added, 5068 seeds are put forward Round 1: 379 peptides, 64 chains. Longest chain 15 peptides. Score 0.443 Round 2: 424 peptides, 61 chains. Longest chain 17 peptides. Score 0.549 Round 3: 428 peptides, 57 chains. Longest chain 34 peptides. Score 0.585 Round 4: 412 peptides, 57 chains. Longest chain 23 peptides. Score 0.559 Round 5: 418 peptides, 51 chains. Longest chain 27 peptides. Score 0.611 Taking the results from Round 5 Chains 51, Residues 367, Estimated correctness of the model 44.0 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 10855 restraints for refining 4973 atoms. 9308 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2618 (Rfree = 0.000) for 4973 atoms. Found 42 (44 requested) and removed 38 (22 requested) atoms. Cycle 7: After refmac, R = 0.2585 (Rfree = 0.000) for 4961 atoms. Found 25 (44 requested) and removed 29 (22 requested) atoms. Cycle 8: After refmac, R = 0.2474 (Rfree = 0.000) for 4947 atoms. Found 22 (44 requested) and removed 28 (22 requested) atoms. Cycle 9: After refmac, R = 0.2374 (Rfree = 0.000) for 4928 atoms. Found 18 (44 requested) and removed 27 (22 requested) atoms. Cycle 10: After refmac, R = 0.2304 (Rfree = 0.000) for 4905 atoms. Found 19 (44 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.09 3.01 Search for helices and strands: 0 residues in 0 chains, 5138 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 5154 seeds are put forward Round 1: 353 peptides, 57 chains. Longest chain 18 peptides. Score 0.451 Round 2: 410 peptides, 55 chains. Longest chain 17 peptides. Score 0.570 Round 3: 410 peptides, 56 chains. Longest chain 32 peptides. Score 0.563 Round 4: 412 peptides, 59 chains. Longest chain 18 peptides. Score 0.544 Round 5: 395 peptides, 57 chains. Longest chain 22 peptides. Score 0.529 Taking the results from Round 2 Chains 55, Residues 355, Estimated correctness of the model 32.7 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 10890 restraints for refining 4973 atoms. 9456 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2394 (Rfree = 0.000) for 4973 atoms. Found 44 (44 requested) and removed 34 (22 requested) atoms. Cycle 12: After refmac, R = 0.2293 (Rfree = 0.000) for 4970 atoms. Found 18 (44 requested) and removed 26 (22 requested) atoms. Cycle 13: After refmac, R = 0.2248 (Rfree = 0.000) for 4951 atoms. Found 16 (44 requested) and removed 25 (22 requested) atoms. Cycle 14: After refmac, R = 0.2174 (Rfree = 0.000) for 4926 atoms. Found 21 (44 requested) and removed 27 (22 requested) atoms. Cycle 15: After refmac, R = 0.2117 (Rfree = 0.000) for 4916 atoms. Found 10 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 3.00 Search for helices and strands: 0 residues in 0 chains, 5103 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 5110 seeds are put forward Round 1: 344 peptides, 59 chains. Longest chain 17 peptides. Score 0.416 Round 2: 396 peptides, 57 chains. Longest chain 20 peptides. Score 0.531 Round 3: 399 peptides, 58 chains. Longest chain 21 peptides. Score 0.529 Round 4: 410 peptides, 57 chains. Longest chain 24 peptides. Score 0.555 Round 5: 412 peptides, 56 chains. Longest chain 23 peptides. Score 0.566 Taking the results from Round 5 Chains 57, Residues 356, Estimated correctness of the model 31.6 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 10725 restraints for refining 4973 atoms. 9271 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2475 (Rfree = 0.000) for 4973 atoms. Found 44 (44 requested) and removed 45 (22 requested) atoms. Cycle 17: After refmac, R = 0.2307 (Rfree = 0.000) for 4952 atoms. Found 22 (44 requested) and removed 29 (22 requested) atoms. Cycle 18: After refmac, R = 0.2209 (Rfree = 0.000) for 4932 atoms. Found 14 (44 requested) and removed 24 (22 requested) atoms. Cycle 19: After refmac, R = 0.2157 (Rfree = 0.000) for 4914 atoms. Found 15 (44 requested) and removed 22 (22 requested) atoms. Cycle 20: After refmac, R = 0.2133 (Rfree = 0.000) for 4904 atoms. Found 12 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 3.00 Search for helices and strands: 0 residues in 0 chains, 5116 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 5149 seeds are put forward Round 1: 328 peptides, 55 chains. Longest chain 18 peptides. Score 0.418 Round 2: 384 peptides, 58 chains. Longest chain 20 peptides. Score 0.502 Round 3: 360 peptides, 54 chains. Longest chain 17 peptides. Score 0.490 Round 4: 376 peptides, 57 chains. Longest chain 17 peptides. Score 0.495 Round 5: 381 peptides, 52 chains. Longest chain 21 peptides. Score 0.544 Taking the results from Round 5 Chains 54, Residues 329, Estimated correctness of the model 25.1 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 10627 restraints for refining 4974 atoms. 9219 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2573 (Rfree = 0.000) for 4974 atoms. Found 44 (44 requested) and removed 37 (22 requested) atoms. Cycle 22: After refmac, R = 0.2351 (Rfree = 0.000) for 4969 atoms. Found 23 (44 requested) and removed 28 (22 requested) atoms. Cycle 23: After refmac, R = 0.2229 (Rfree = 0.000) for 4954 atoms. Found 12 (44 requested) and removed 22 (22 requested) atoms. Cycle 24: After refmac, R = 0.2164 (Rfree = 0.000) for 4936 atoms. Found 16 (44 requested) and removed 25 (22 requested) atoms. Cycle 25: After refmac, R = 0.2112 (Rfree = 0.000) for 4921 atoms. Found 7 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.07 2.99 Search for helices and strands: 0 residues in 0 chains, 5149 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 5163 seeds are put forward Round 1: 318 peptides, 59 chains. Longest chain 13 peptides. Score 0.361 Round 2: 338 peptides, 49 chains. Longest chain 19 peptides. Score 0.490 Round 3: 348 peptides, 54 chains. Longest chain 20 peptides. Score 0.467 Round 4: 330 peptides, 50 chains. Longest chain 15 peptides. Score 0.466 Round 5: 371 peptides, 56 chains. Longest chain 20 peptides. Score 0.494 Taking the results from Round 5 Chains 56, Residues 315, Estimated correctness of the model 9.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 11337 restraints for refining 4974 atoms. 10133 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2389 (Rfree = 0.000) for 4974 atoms. Found 44 (44 requested) and removed 24 (22 requested) atoms. Cycle 27: After refmac, R = 0.2243 (Rfree = 0.000) for 4990 atoms. Found 17 (44 requested) and removed 23 (22 requested) atoms. Cycle 28: After refmac, R = 0.2179 (Rfree = 0.000) for 4979 atoms. Found 7 (44 requested) and removed 22 (22 requested) atoms. Cycle 29: After refmac, R = 0.2170 (Rfree = 0.000) for 4962 atoms. Found 9 (44 requested) and removed 22 (22 requested) atoms. Cycle 30: After refmac, R = 0.2163 (Rfree = 0.000) for 4948 atoms. Found 13 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 2.99 Search for helices and strands: 0 residues in 0 chains, 5158 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 5176 seeds are put forward Round 1: 307 peptides, 54 chains. Longest chain 13 peptides. Score 0.383 Round 2: 351 peptides, 53 chains. Longest chain 20 peptides. Score 0.481 Round 3: 361 peptides, 58 chains. Longest chain 13 peptides. Score 0.458 Round 4: 368 peptides, 54 chains. Longest chain 23 peptides. Score 0.505 Round 5: 361 peptides, 53 chains. Longest chain 25 peptides. Score 0.500 Taking the results from Round 4 Chains 54, Residues 314, Estimated correctness of the model 12.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 11165 restraints for refining 4973 atoms. 9963 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2378 (Rfree = 0.000) for 4973 atoms. Found 39 (44 requested) and removed 23 (22 requested) atoms. Cycle 32: After refmac, R = 0.2263 (Rfree = 0.000) for 4984 atoms. Found 10 (44 requested) and removed 25 (22 requested) atoms. Cycle 33: After refmac, R = 0.2213 (Rfree = 0.000) for 4965 atoms. Found 14 (44 requested) and removed 22 (22 requested) atoms. Cycle 34: After refmac, R = 0.2206 (Rfree = 0.000) for 4953 atoms. Found 8 (44 requested) and removed 22 (22 requested) atoms. Cycle 35: After refmac, R = 0.2178 (Rfree = 0.000) for 4936 atoms. Found 11 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.07 2.99 Search for helices and strands: 0 residues in 0 chains, 5144 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 5169 seeds are put forward Round 1: 291 peptides, 55 chains. Longest chain 13 peptides. Score 0.339 Round 2: 348 peptides, 57 chains. Longest chain 15 peptides. Score 0.441 Round 3: 344 peptides, 54 chains. Longest chain 13 peptides. Score 0.459 Round 4: 353 peptides, 55 chains. Longest chain 16 peptides. Score 0.468 Round 5: 347 peptides, 54 chains. Longest chain 18 peptides. Score 0.465 Taking the results from Round 4 Chains 55, Residues 298, Estimated correctness of the model 0.7 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 11260 restraints for refining 4974 atoms. 10097 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2378 (Rfree = 0.000) for 4974 atoms. Found 33 (44 requested) and removed 24 (22 requested) atoms. Cycle 37: After refmac, R = 0.2305 (Rfree = 0.000) for 4972 atoms. Found 27 (44 requested) and removed 26 (22 requested) atoms. Cycle 38: After refmac, R = 0.2081 (Rfree = 0.000) for 4967 atoms. Found 16 (44 requested) and removed 25 (22 requested) atoms. Cycle 39: After refmac, R = 0.2042 (Rfree = 0.000) for 4954 atoms. Found 15 (44 requested) and removed 24 (22 requested) atoms. Cycle 40: After refmac, R = 0.1978 (Rfree = 0.000) for 4937 atoms. Found 16 (44 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.06 2.98 Search for helices and strands: 0 residues in 0 chains, 5144 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 5163 seeds are put forward Round 1: 279 peptides, 52 chains. Longest chain 15 peptides. Score 0.341 Round 2: 332 peptides, 57 chains. Longest chain 12 peptides. Score 0.409 Round 3: 309 peptides, 52 chains. Longest chain 13 peptides. Score 0.406 Round 4: 341 peptides, 52 chains. Longest chain 15 peptides. Score 0.470 Round 5: 351 peptides, 54 chains. Longest chain 18 peptides. Score 0.473 Taking the results from Round 5 Chains 54, Residues 297, Estimated correctness of the model 2.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 11080 restraints for refining 4974 atoms. 9946 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2213 (Rfree = 0.000) for 4974 atoms. Found 39 (44 requested) and removed 26 (22 requested) atoms. Cycle 42: After refmac, R = 0.2093 (Rfree = 0.000) for 4980 atoms. Found 16 (44 requested) and removed 25 (22 requested) atoms. Cycle 43: After refmac, R = 0.2031 (Rfree = 0.000) for 4964 atoms. Found 16 (44 requested) and removed 22 (22 requested) atoms. Cycle 44: After refmac, R = 0.1992 (Rfree = 0.000) for 4951 atoms. Found 11 (44 requested) and removed 22 (22 requested) atoms. Cycle 45: After refmac, R = 0.1957 (Rfree = 0.000) for 4938 atoms. Found 9 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.06 2.98 Search for helices and strands: 0 residues in 0 chains, 5138 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 5165 seeds are put forward Round 1: 284 peptides, 55 chains. Longest chain 12 peptides. Score 0.323 Round 2: 297 peptides, 49 chains. Longest chain 13 peptides. Score 0.408 Round 3: 304 peptides, 45 chains. Longest chain 13 peptides. Score 0.458 Round 4: 310 peptides, 49 chains. Longest chain 14 peptides. Score 0.435 Round 5: 318 peptides, 52 chains. Longest chain 14 peptides. Score 0.425 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 259, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2iiu-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12997 reflections ( 99.27 % complete ) and 11467 restraints for refining 4973 atoms. 10424 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2140 (Rfree = 0.000) for 4973 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.2087 (Rfree = 0.000) for 4945 atoms. Found 0 (44 requested) and removed 19 (22 requested) atoms. Cycle 48: After refmac, R = 0.2051 (Rfree = 0.000) for 4919 atoms. Found 0 (44 requested) and removed 11 (22 requested) atoms. Cycle 49: After refmac, R = 0.1995 (Rfree = 0.000) for 4905 atoms. Found 0 (44 requested) and removed 11 (22 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:50:19 GMT 2018 Job finished. TimeTaking 60.8 Used memory is bytes: 18059032