Sun 23 Dec 23:44:59 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 1z82-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1z82-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1z82-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-3.6-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/1z82-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-3.6-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 23:45:04 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/1z82-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-3.6-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 400 and 0 Target number of residues in the AU: 400 Target solvent content: 0.6446 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.40 Input MTZ file: 1z82-3.6-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: 4 Cell parameters: 65.170 67.461 75.617 90.000 113.643 90.000 Input sequence file: 1z82-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5360 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: 29.850 3.600 Wilson plot Bfac: 74.45 7073 reflections ( 99.58 % complete ) and 0 restraints for refining 5938 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3068 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2749 (Rfree = 0.000) for 5938 atoms. Found 34 (38 requested) and removed 45 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.98 Search for helices and strands: 0 residues in 0 chains, 6056 seeds are put forward NCS extension: 0 residues added, 6056 seeds are put forward Round 1: 196 peptides, 41 chains. Longest chain 12 peptides. Score 0.269 Round 2: 288 peptides, 54 chains. Longest chain 13 peptides. Score 0.374 Round 3: 325 peptides, 52 chains. Longest chain 17 peptides. Score 0.488 Round 4: 344 peptides, 57 chains. Longest chain 16 peptides. Score 0.482 Round 5: 348 peptides, 51 chains. Longest chain 22 peptides. Score 0.548 Taking the results from Round 5 Chains 52, Residues 297, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 11093 restraints for refining 4858 atoms. 9875 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2451 (Rfree = 0.000) for 4858 atoms. Found 31 (31 requested) and removed 37 (15 requested) atoms. Cycle 2: After refmac, R = 0.2336 (Rfree = 0.000) for 4790 atoms. Found 31 (31 requested) and removed 30 (15 requested) atoms. Cycle 3: After refmac, R = 0.2294 (Rfree = 0.000) for 4756 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. Cycle 4: After refmac, R = 0.2188 (Rfree = 0.000) for 4732 atoms. Found 27 (30 requested) and removed 27 (15 requested) atoms. Cycle 5: After refmac, R = 0.1764 (Rfree = 0.000) for 4703 atoms. Found 12 (30 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.95 Search for helices and strands: 0 residues in 0 chains, 4891 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4905 seeds are put forward Round 1: 229 peptides, 45 chains. Longest chain 11 peptides. Score 0.317 Round 2: 301 peptides, 53 chains. Longest chain 15 peptides. Score 0.419 Round 3: 331 peptides, 50 chains. Longest chain 15 peptides. Score 0.521 Round 4: 331 peptides, 52 chains. Longest chain 17 peptides. Score 0.501 Round 5: 334 peptides, 51 chains. Longest chain 16 peptides. Score 0.518 Taking the results from Round 3 Chains 52, Residues 281, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 10396 restraints for refining 4574 atoms. 9261 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1935 (Rfree = 0.000) for 4574 atoms. Found 29 (29 requested) and removed 47 (14 requested) atoms. Cycle 7: After refmac, R = 0.1861 (Rfree = 0.000) for 4532 atoms. Found 23 (29 requested) and removed 30 (14 requested) atoms. Cycle 8: After refmac, R = 0.1883 (Rfree = 0.000) for 4511 atoms. Found 20 (29 requested) and removed 24 (14 requested) atoms. Cycle 9: After refmac, R = 0.1891 (Rfree = 0.000) for 4501 atoms. Found 26 (28 requested) and removed 22 (14 requested) atoms. Cycle 10: After refmac, R = 0.1864 (Rfree = 0.000) for 4495 atoms. Found 23 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.99 Search for helices and strands: 0 residues in 0 chains, 4661 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4674 seeds are put forward Round 1: 287 peptides, 55 chains. Longest chain 11 peptides. Score 0.361 Round 2: 309 peptides, 50 chains. Longest chain 19 peptides. Score 0.470 Round 3: 320 peptides, 50 chains. Longest chain 15 peptides. Score 0.496 Round 4: 320 peptides, 51 chains. Longest chain 16 peptides. Score 0.486 Round 5: 317 peptides, 46 chains. Longest chain 15 peptides. Score 0.529 Taking the results from Round 5 Chains 47, Residues 271, Estimated correctness of the model 0.0 % 4 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 10950 restraints for refining 4703 atoms. 9832 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2104 (Rfree = 0.000) for 4703 atoms. Found 24 (30 requested) and removed 54 (15 requested) atoms. Cycle 12: After refmac, R = 0.1919 (Rfree = 0.000) for 4642 atoms. Found 15 (29 requested) and removed 21 (14 requested) atoms. Cycle 13: After refmac, R = 0.1892 (Rfree = 0.000) for 4618 atoms. Found 22 (29 requested) and removed 23 (14 requested) atoms. Cycle 14: After refmac, R = 0.1825 (Rfree = 0.000) for 4607 atoms. Found 17 (29 requested) and removed 22 (14 requested) atoms. Cycle 15: After refmac, R = 0.1786 (Rfree = 0.000) for 4594 atoms. Found 15 (29 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.94 Search for helices and strands: 0 residues in 0 chains, 4792 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 4815 seeds are put forward Round 1: 277 peptides, 53 chains. Longest chain 13 peptides. Score 0.356 Round 2: 310 peptides, 52 chains. Longest chain 13 peptides. Score 0.452 Round 3: 303 peptides, 46 chains. Longest chain 16 peptides. Score 0.497 Round 4: 309 peptides, 45 chains. Longest chain 15 peptides. Score 0.521 Round 5: 311 peptides, 49 chains. Longest chain 17 peptides. Score 0.485 Taking the results from Round 4 Chains 45, Residues 264, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 10956 restraints for refining 4663 atoms. 9945 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1863 (Rfree = 0.000) for 4663 atoms. Found 23 (29 requested) and removed 31 (14 requested) atoms. Cycle 17: After refmac, R = 0.1769 (Rfree = 0.000) for 4633 atoms. Found 14 (29 requested) and removed 25 (14 requested) atoms. Cycle 18: After refmac, R = 0.1746 (Rfree = 0.000) for 4616 atoms. Found 16 (29 requested) and removed 16 (14 requested) atoms. Cycle 19: After refmac, R = 0.1692 (Rfree = 0.000) for 4608 atoms. Found 19 (29 requested) and removed 20 (14 requested) atoms. Cycle 20: After refmac, R = 0.1719 (Rfree = 0.000) for 4591 atoms. Found 20 (29 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.96 Search for helices and strands: 0 residues in 0 chains, 4783 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4798 seeds are put forward Round 1: 248 peptides, 48 chains. Longest chain 11 peptides. Score 0.335 Round 2: 284 peptides, 46 chains. Longest chain 14 peptides. Score 0.452 Round 3: 306 peptides, 47 chains. Longest chain 16 peptides. Score 0.494 Round 4: 316 peptides, 46 chains. Longest chain 16 peptides. Score 0.526 Round 5: 312 peptides, 43 chains. Longest chain 14 peptides. Score 0.547 Taking the results from Round 5 Chains 43, Residues 269, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 10732 restraints for refining 4681 atoms. 9681 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1860 (Rfree = 0.000) for 4681 atoms. Found 28 (30 requested) and removed 34 (15 requested) atoms. Cycle 22: After refmac, R = 0.1706 (Rfree = 0.000) for 4659 atoms. Found 14 (29 requested) and removed 19 (14 requested) atoms. Cycle 23: After refmac, R = 0.1654 (Rfree = 0.000) for 4649 atoms. Found 12 (29 requested) and removed 20 (14 requested) atoms. Cycle 24: After refmac, R = 0.1666 (Rfree = 0.000) for 4637 atoms. Found 10 (29 requested) and removed 24 (14 requested) atoms. Cycle 25: After refmac, R = 0.1618 (Rfree = 0.000) for 4617 atoms. Found 11 (29 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.95 Search for helices and strands: 0 residues in 0 chains, 4799 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4813 seeds are put forward Round 1: 230 peptides, 46 chains. Longest chain 12 peptides. Score 0.307 Round 2: 251 peptides, 39 chains. Longest chain 14 peptides. Score 0.445 Round 3: 281 peptides, 45 chains. Longest chain 15 peptides. Score 0.455 Round 4: 279 peptides, 45 chains. Longest chain 15 peptides. Score 0.450 Round 5: 277 peptides, 44 chains. Longest chain 15 peptides. Score 0.456 Taking the results from Round 5 Chains 44, Residues 233, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 10906 restraints for refining 4670 atoms. 9997 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1750 (Rfree = 0.000) for 4670 atoms. Found 14 (29 requested) and removed 36 (14 requested) atoms. Cycle 27: After refmac, R = 0.1618 (Rfree = 0.000) for 4630 atoms. Found 6 (29 requested) and removed 18 (14 requested) atoms. Cycle 28: After refmac, R = 0.1592 (Rfree = 0.000) for 4614 atoms. Found 9 (29 requested) and removed 16 (14 requested) atoms. Cycle 29: After refmac, R = 0.1573 (Rfree = 0.000) for 4601 atoms. Found 13 (29 requested) and removed 18 (14 requested) atoms. Cycle 30: After refmac, R = 0.1512 (Rfree = 0.000) for 4591 atoms. Found 7 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.98 Search for helices and strands: 0 residues in 0 chains, 4760 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4783 seeds are put forward Round 1: 245 peptides, 50 chains. Longest chain 12 peptides. Score 0.302 Round 2: 279 peptides, 45 chains. Longest chain 16 peptides. Score 0.450 Round 3: 296 peptides, 48 chains. Longest chain 15 peptides. Score 0.460 Round 4: 286 peptides, 46 chains. Longest chain 26 peptides. Score 0.456 Round 5: 282 peptides, 47 chains. Longest chain 16 peptides. Score 0.436 Taking the results from Round 3 Chains 48, Residues 248, Estimated correctness of the model 0.0 % 4 chains (29 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 10702 restraints for refining 4688 atoms. 9661 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1715 (Rfree = 0.000) for 4688 atoms. Found 15 (30 requested) and removed 34 (15 requested) atoms. Cycle 32: After refmac, R = 0.1573 (Rfree = 0.000) for 4661 atoms. Found 5 (29 requested) and removed 22 (14 requested) atoms. Cycle 33: After refmac, R = 0.1535 (Rfree = 0.000) for 4641 atoms. Found 11 (29 requested) and removed 18 (14 requested) atoms. Cycle 34: After refmac, R = 0.1509 (Rfree = 0.000) for 4629 atoms. Found 7 (29 requested) and removed 20 (14 requested) atoms. Cycle 35: After refmac, R = 0.1553 (Rfree = 0.000) for 4613 atoms. Found 11 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.94 Search for helices and strands: 0 residues in 0 chains, 4814 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 4836 seeds are put forward Round 1: 221 peptides, 46 chains. Longest chain 12 peptides. Score 0.281 Round 2: 258 peptides, 44 chains. Longest chain 19 peptides. Score 0.408 Round 3: 255 peptides, 45 chains. Longest chain 13 peptides. Score 0.388 Round 4: 248 peptides, 46 chains. Longest chain 13 peptides. Score 0.358 Round 5: 270 peptides, 47 chains. Longest chain 15 peptides. Score 0.405 Taking the results from Round 2 Chains 45, Residues 214, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 10932 restraints for refining 4694 atoms. 10049 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1556 (Rfree = 0.000) for 4694 atoms. Found 9 (30 requested) and removed 26 (15 requested) atoms. Cycle 37: After refmac, R = 0.1561 (Rfree = 0.000) for 4666 atoms. Found 8 (30 requested) and removed 17 (15 requested) atoms. Cycle 38: After refmac, R = 0.1494 (Rfree = 0.000) for 4647 atoms. Found 8 (29 requested) and removed 17 (14 requested) atoms. Cycle 39: After refmac, R = 0.1540 (Rfree = 0.000) for 4633 atoms. Found 11 (29 requested) and removed 16 (14 requested) atoms. Cycle 40: After refmac, R = 0.1469 (Rfree = 0.000) for 4624 atoms. Found 10 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.93 Search for helices and strands: 0 residues in 0 chains, 4799 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 4817 seeds are put forward Round 1: 173 peptides, 32 chains. Longest chain 12 peptides. Score 0.315 Round 2: 205 peptides, 35 chains. Longest chain 13 peptides. Score 0.370 Round 3: 227 peptides, 39 chains. Longest chain 16 peptides. Score 0.383 Round 4: 221 peptides, 36 chains. Longest chain 16 peptides. Score 0.402 Round 5: 229 peptides, 35 chains. Longest chain 18 peptides. Score 0.434 Taking the results from Round 5 Chains 35, Residues 194, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 11257 restraints for refining 4711 atoms. 10483 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1630 (Rfree = 0.000) for 4711 atoms. Found 11 (30 requested) and removed 26 (15 requested) atoms. Cycle 42: After refmac, R = 0.1546 (Rfree = 0.000) for 4686 atoms. Found 10 (30 requested) and removed 17 (15 requested) atoms. Cycle 43: After refmac, R = 0.1575 (Rfree = 0.000) for 4674 atoms. Found 8 (30 requested) and removed 20 (15 requested) atoms. Cycle 44: After refmac, R = 0.1596 (Rfree = 0.000) for 4658 atoms. Found 19 (29 requested) and removed 17 (14 requested) atoms. Cycle 45: After refmac, R = 0.1514 (Rfree = 0.000) for 4657 atoms. Found 12 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.97 Search for helices and strands: 0 residues in 0 chains, 4823 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4841 seeds are put forward Round 1: 211 peptides, 46 chains. Longest chain 10 peptides. Score 0.251 Round 2: 205 peptides, 38 chains. Longest chain 12 peptides. Score 0.333 Round 3: 210 peptides, 35 chains. Longest chain 18 peptides. Score 0.384 Round 4: 197 peptides, 33 chains. Longest chain 13 peptides. Score 0.372 Round 5: 203 peptides, 33 chains. Longest chain 23 peptides. Score 0.389 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 170, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1z82-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7073 reflections ( 99.58 % complete ) and 11347 restraints for refining 4741 atoms. 10675 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1615 (Rfree = 0.000) for 4741 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.1394 (Rfree = 0.000) for 4721 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1392 (Rfree = 0.000) for 4703 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1328 (Rfree = 0.000) for 4687 atoms. TimeTaking 56.95