Mon 24 Dec 00:28:37 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 1ztc-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1ztc-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1ztc-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1ztc-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/1ztc-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1ztc-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 ============================================================ Mon 24 Dec 00:28:42 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/1ztc-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1ztc-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 1067 and 0 Target number of residues in the AU: 1067 Target solvent content: 0.6682 Checking the provided sequence file Detected sequence length: 221 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 884 Adjusted target solvent content: 0.73 Input MTZ file: 1ztc-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: 19 Cell parameters: 89.783 127.343 152.224 90.000 90.000 90.000 Input sequence file: 1ztc-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7072 target number of atoms Had to go as low as 1.10 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: 97.673 4.000 Wilson plot Bfac: 91.02 15050 reflections ( 98.31 % complete ) and 0 restraints for refining 7906 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3390 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3321 (Rfree = 0.000) for 7906 atoms. Found 37 (37 requested) and removed 30 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.82 2.74 Search for helices and strands: 0 residues in 0 chains, 8058 seeds are put forward NCS extension: 0 residues added, 8058 seeds are put forward Round 1: 476 peptides, 70 chains. Longest chain 14 peptides. Score 0.394 Round 2: 569 peptides, 68 chains. Longest chain 24 peptides. Score 0.488 Round 3: 601 peptides, 59 chains. Longest chain 26 peptides. Score 0.550 Round 4: 596 peptides, 56 chains. Longest chain 25 peptides. Score 0.557 Round 5: 588 peptides, 57 chains. Longest chain 36 peptides. Score 0.547 Taking the results from Round 4 Chains 56, Residues 540, Estimated correctness of the model 0.0 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 13755 restraints for refining 6387 atoms. 11517 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2853 (Rfree = 0.000) for 6387 atoms. Found 30 (30 requested) and removed 29 (15 requested) atoms. Cycle 2: After refmac, R = 0.2590 (Rfree = 0.000) for 6262 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. Cycle 3: After refmac, R = 0.2413 (Rfree = 0.000) for 6205 atoms. Found 29 (29 requested) and removed 31 (14 requested) atoms. Cycle 4: After refmac, R = 0.2330 (Rfree = 0.000) for 6175 atoms. Found 29 (29 requested) and removed 33 (14 requested) atoms. Cycle 5: After refmac, R = 0.2234 (Rfree = 0.000) for 6148 atoms. Found 19 (29 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.78 2.71 Search for helices and strands: 0 residues in 0 chains, 6356 seeds are put forward NCS extension: 42 residues added (2 deleted due to clashes), 6398 seeds are put forward Round 1: 564 peptides, 65 chains. Longest chain 28 peptides. Score 0.496 Round 2: 571 peptides, 55 chains. Longest chain 51 peptides. Score 0.541 Round 3: 563 peptides, 57 chains. Longest chain 31 peptides. Score 0.527 Round 4: 558 peptides, 52 chains. Longest chain 37 peptides. Score 0.543 Round 5: 578 peptides, 56 chains. Longest chain 34 peptides. Score 0.543 Taking the results from Round 5 Chains 59, Residues 522, Estimated correctness of the model 0.0 % 3 chains (57 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 13435 restraints for refining 6386 atoms. 11159 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2639 (Rfree = 0.000) for 6386 atoms. Found 30 (30 requested) and removed 37 (15 requested) atoms. Cycle 7: After refmac, R = 0.2459 (Rfree = 0.000) for 6327 atoms. Found 30 (30 requested) and removed 34 (15 requested) atoms. Cycle 8: After refmac, R = 0.2306 (Rfree = 0.000) for 6301 atoms. Found 19 (30 requested) and removed 49 (15 requested) atoms. Cycle 9: After refmac, R = 0.2274 (Rfree = 0.000) for 6253 atoms. Found 27 (29 requested) and removed 23 (14 requested) atoms. Cycle 10: After refmac, R = 0.2240 (Rfree = 0.000) for 6243 atoms. Found 29 (29 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.81 2.74 Search for helices and strands: 0 residues in 0 chains, 6509 seeds are put forward NCS extension: 32 residues added (6 deleted due to clashes), 6541 seeds are put forward Round 1: 566 peptides, 64 chains. Longest chain 27 peptides. Score 0.502 Round 2: 593 peptides, 58 chains. Longest chain 35 peptides. Score 0.547 Round 3: 593 peptides, 61 chains. Longest chain 24 peptides. Score 0.536 Round 4: 617 peptides, 54 chains. Longest chain 34 peptides. Score 0.581 Round 5: 618 peptides, 55 chains. Longest chain 35 peptides. Score 0.578 Taking the results from Round 4 Chains 55, Residues 563, Estimated correctness of the model 0.0 % 2 chains (61 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 13266 restraints for refining 6385 atoms. 10799 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2630 (Rfree = 0.000) for 6385 atoms. Found 30 (30 requested) and removed 28 (15 requested) atoms. Cycle 12: After refmac, R = 0.2400 (Rfree = 0.000) for 6293 atoms. Found 21 (30 requested) and removed 28 (15 requested) atoms. Cycle 13: After refmac, R = 0.2311 (Rfree = 0.000) for 6241 atoms. Found 29 (29 requested) and removed 108 (14 requested) atoms. Cycle 14: After refmac, R = 0.2281 (Rfree = 0.000) for 6142 atoms. Found 26 (29 requested) and removed 17 (14 requested) atoms. Cycle 15: After refmac, R = 0.2219 (Rfree = 0.000) for 6132 atoms. Found 11 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.83 2.75 Search for helices and strands: 0 residues in 0 chains, 6325 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 6353 seeds are put forward Round 1: 567 peptides, 67 chains. Longest chain 35 peptides. Score 0.490 Round 2: 606 peptides, 56 chains. Longest chain 34 peptides. Score 0.565 Round 3: 591 peptides, 59 chains. Longest chain 34 peptides. Score 0.542 Round 4: 595 peptides, 57 chains. Longest chain 35 peptides. Score 0.553 Round 5: 562 peptides, 50 chains. Longest chain 42 peptides. Score 0.554 Taking the results from Round 2 Chains 57, Residues 550, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 13600 restraints for refining 6386 atoms. 11359 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2476 (Rfree = 0.000) for 6386 atoms. Found 30 (30 requested) and removed 19 (15 requested) atoms. Cycle 17: After refmac, R = 0.2336 (Rfree = 0.000) for 6316 atoms. Found 20 (30 requested) and removed 38 (15 requested) atoms. Cycle 18: After refmac, R = 0.2289 (Rfree = 0.000) for 6271 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. Cycle 19: After refmac, R = 0.2254 (Rfree = 0.000) for 6261 atoms. Found 22 (29 requested) and removed 24 (14 requested) atoms. Cycle 20: After refmac, R = 0.2232 (Rfree = 0.000) for 6235 atoms. Found 24 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 2.74 Search for helices and strands: 0 residues in 0 chains, 6428 seeds are put forward NCS extension: 30 residues added (8 deleted due to clashes), 6458 seeds are put forward Round 1: 558 peptides, 66 chains. Longest chain 27 peptides. Score 0.486 Round 2: 565 peptides, 57 chains. Longest chain 33 peptides. Score 0.529 Round 3: 567 peptides, 59 chains. Longest chain 34 peptides. Score 0.522 Round 4: 572 peptides, 54 chains. Longest chain 35 peptides. Score 0.546 Round 5: 577 peptides, 58 chains. Longest chain 38 peptides. Score 0.534 Taking the results from Round 4 Chains 55, Residues 518, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 14216 restraints for refining 6386 atoms. 12141 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2572 (Rfree = 0.000) for 6386 atoms. Found 30 (30 requested) and removed 41 (15 requested) atoms. Cycle 22: After refmac, R = 0.2342 (Rfree = 0.000) for 6306 atoms. Found 30 (30 requested) and removed 34 (15 requested) atoms. Cycle 23: After refmac, R = 0.2285 (Rfree = 0.000) for 6275 atoms. Found 29 (29 requested) and removed 20 (14 requested) atoms. Cycle 24: After refmac, R = 0.2239 (Rfree = 0.000) for 6249 atoms. Found 29 (29 requested) and removed 42 (14 requested) atoms. Cycle 25: After refmac, R = 0.2191 (Rfree = 0.000) for 6215 atoms. Found 29 (29 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.79 2.72 Search for helices and strands: 0 residues in 0 chains, 6423 seeds are put forward NCS extension: 37 residues added (17 deleted due to clashes), 6460 seeds are put forward Round 1: 555 peptides, 70 chains. Longest chain 26 peptides. Score 0.467 Round 2: 574 peptides, 60 chains. Longest chain 37 peptides. Score 0.524 Round 3: 569 peptides, 61 chains. Longest chain 44 peptides. Score 0.516 Round 4: 565 peptides, 55 chains. Longest chain 35 peptides. Score 0.537 Round 5: 562 peptides, 57 chains. Longest chain 42 peptides. Score 0.526 Taking the results from Round 4 Chains 55, Residues 510, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 14375 restraints for refining 6384 atoms. 12390 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2715 (Rfree = 0.000) for 6384 atoms. Found 30 (30 requested) and removed 28 (15 requested) atoms. Cycle 27: After refmac, R = 0.2566 (Rfree = 0.000) for 6297 atoms. Found 30 (30 requested) and removed 21 (15 requested) atoms. Cycle 28: After refmac, R = 0.2402 (Rfree = 0.000) for 6255 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. Cycle 29: After refmac, R = 0.2419 (Rfree = 0.000) for 6224 atoms. Found 29 (29 requested) and removed 18 (14 requested) atoms. Cycle 30: After refmac, R = 0.2276 (Rfree = 0.000) for 6211 atoms. Found 29 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.84 2.76 Search for helices and strands: 0 residues in 0 chains, 6441 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 6456 seeds are put forward Round 1: 504 peptides, 69 chains. Longest chain 18 peptides. Score 0.425 Round 2: 557 peptides, 66 chains. Longest chain 24 peptides. Score 0.486 Round 3: 573 peptides, 70 chains. Longest chain 22 peptides. Score 0.483 Round 4: 558 peptides, 59 chains. Longest chain 32 peptides. Score 0.515 Round 5: 582 peptides, 62 chains. Longest chain 27 peptides. Score 0.523 Taking the results from Round 5 Chains 68, Residues 520, Estimated correctness of the model 0.0 % 3 chains (46 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 13616 restraints for refining 6387 atoms. 11399 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2584 (Rfree = 0.000) for 6387 atoms. Found 30 (30 requested) and removed 27 (15 requested) atoms. Cycle 32: After refmac, R = 0.2405 (Rfree = 0.000) for 6302 atoms. Found 30 (30 requested) and removed 26 (15 requested) atoms. Cycle 33: After refmac, R = 0.2370 (Rfree = 0.000) for 6258 atoms. Found 29 (29 requested) and removed 31 (14 requested) atoms. Cycle 34: After refmac, R = 0.2343 (Rfree = 0.000) for 6238 atoms. Found 29 (29 requested) and removed 20 (14 requested) atoms. Cycle 35: After refmac, R = 0.2313 (Rfree = 0.000) for 6207 atoms. Found 29 (29 requested) and removed 28 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.83 2.75 Search for helices and strands: 0 residues in 0 chains, 6419 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6432 seeds are put forward Round 1: 530 peptides, 75 chains. Longest chain 19 peptides. Score 0.423 Round 2: 559 peptides, 66 chains. Longest chain 25 peptides. Score 0.487 Round 3: 564 peptides, 63 chains. Longest chain 44 peptides. Score 0.504 Round 4: 548 peptides, 56 chains. Longest chain 28 peptides. Score 0.519 Round 5: 563 peptides, 58 chains. Longest chain 25 peptides. Score 0.523 Taking the results from Round 5 Chains 59, Residues 505, Estimated correctness of the model 0.0 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 14184 restraints for refining 6386 atoms. 12120 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2751 (Rfree = 0.000) for 6386 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. Cycle 37: After refmac, R = 0.2420 (Rfree = 0.000) for 6297 atoms. Found 30 (30 requested) and removed 20 (15 requested) atoms. Cycle 38: After refmac, R = 0.2336 (Rfree = 0.000) for 6256 atoms. Found 29 (29 requested) and removed 20 (14 requested) atoms. Cycle 39: After refmac, R = 0.2262 (Rfree = 0.000) for 6241 atoms. Found 29 (29 requested) and removed 15 (14 requested) atoms. Cycle 40: After refmac, R = 0.2273 (Rfree = 0.000) for 6231 atoms. Found 29 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.82 2.74 Search for helices and strands: 0 residues in 0 chains, 6447 seeds are put forward NCS extension: 20 residues added (8 deleted due to clashes), 6467 seeds are put forward Round 1: 474 peptides, 72 chains. Longest chain 20 peptides. Score 0.383 Round 2: 552 peptides, 68 chains. Longest chain 28 peptides. Score 0.473 Round 3: 538 peptides, 68 chains. Longest chain 20 peptides. Score 0.461 Round 4: 533 peptides, 58 chains. Longest chain 24 peptides. Score 0.498 Round 5: 543 peptides, 63 chains. Longest chain 27 peptides. Score 0.486 Taking the results from Round 4 Chains 58, Residues 475, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 14765 restraints for refining 6383 atoms. 12923 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2586 (Rfree = 0.000) for 6383 atoms. Found 30 (30 requested) and removed 19 (15 requested) atoms. Cycle 42: After refmac, R = 0.2342 (Rfree = 0.000) for 6333 atoms. Found 30 (30 requested) and removed 22 (15 requested) atoms. Cycle 43: After refmac, R = 0.2408 (Rfree = 0.000) for 6298 atoms. Found 30 (30 requested) and removed 23 (15 requested) atoms. Cycle 44: After refmac, R = 0.2337 (Rfree = 0.000) for 6276 atoms. Found 29 (29 requested) and removed 20 (14 requested) atoms. Cycle 45: After refmac, R = 0.2347 (Rfree = 0.000) for 6264 atoms. Found 29 (29 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.82 2.74 Search for helices and strands: 0 residues in 0 chains, 6525 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 6552 seeds are put forward Round 1: 484 peptides, 74 chains. Longest chain 15 peptides. Score 0.384 Round 2: 538 peptides, 65 chains. Longest chain 28 peptides. Score 0.473 Round 3: 545 peptides, 65 chains. Longest chain 22 peptides. Score 0.479 Round 4: 544 peptides, 62 chains. Longest chain 34 peptides. Score 0.491 Round 5: 562 peptides, 61 chains. Longest chain 34 peptides. Score 0.510 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 63, Residues 501, Estimated correctness of the model 0.0 % 2 chains (26 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1ztc-4_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 156 A and 165 A 59 chains (503 residues) following loop building 1 chains (34 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15050 reflections ( 98.31 % complete ) and 14024 restraints for refining 6385 atoms. 11960 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2494 (Rfree = 0.000) for 6385 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2454 (Rfree = 0.000) for 6293 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2306 (Rfree = 0.000) for 6237 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2251 (Rfree = 0.000) for 6207 atoms. TimeTaking 84.45