Mon 24 Dec 00:23:03 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 1vkz-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkz-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkz-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-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/1vkz-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-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 00:23:08 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/1vkz-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-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 603 and 0 Target number of residues in the AU: 603 Target solvent content: 0.6147 Checking the provided sequence file Detected sequence length: 412 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 824 Adjusted target solvent content: 0.47 Input MTZ file: 1vkz-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: 4 Cell parameters: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6592 target number of atoms Had to go as low as 0.60 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: 19.959 4.001 Wilson plot Bfac: 58.96 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 6916 reflections ( 96.32 % complete ) and 0 restraints for refining 7313 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.2961 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2959 (Rfree = 0.000) for 7313 atoms. Found 34 (34 requested) and removed 78 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.53 Search for helices and strands: 0 residues in 0 chains, 7356 seeds are put forward NCS extension: 0 residues added, 7356 seeds are put forward Round 1: 222 peptides, 45 chains. Longest chain 11 peptides. Score 0.269 Round 2: 318 peptides, 58 chains. Longest chain 12 peptides. Score 0.355 Round 3: 354 peptides, 57 chains. Longest chain 13 peptides. Score 0.432 Round 4: 385 peptides, 59 chains. Longest chain 19 peptides. Score 0.472 Round 5: 369 peptides, 55 chains. Longest chain 16 peptides. Score 0.475 Taking the results from Round 5 Chains 55, Residues 314, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 13960 restraints for refining 5950 atoms. 12707 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2732 (Rfree = 0.000) for 5950 atoms. Found 28 (28 requested) and removed 52 (14 requested) atoms. Cycle 2: After refmac, R = 0.2553 (Rfree = 0.000) for 5776 atoms. Found 28 (28 requested) and removed 55 (14 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2486 (Rfree = 0.000) for 5673 atoms. Found 27 (27 requested) and removed 49 (13 requested) atoms. Cycle 4: After refmac, R = 0.2382 (Rfree = 0.000) for 5603 atoms. Found 26 (26 requested) and removed 45 (13 requested) atoms. Cycle 5: After refmac, R = 0.2361 (Rfree = 0.000) for 5546 atoms. Found 26 (26 requested) and removed 58 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.55 Search for helices and strands: 0 residues in 0 chains, 5678 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5699 seeds are put forward Round 1: 358 peptides, 69 chains. Longest chain 11 peptides. Score 0.342 Round 2: 396 peptides, 65 chains. Longest chain 14 peptides. Score 0.445 Round 3: 412 peptides, 60 chains. Longest chain 17 peptides. Score 0.510 Round 4: 413 peptides, 63 chains. Longest chain 18 peptides. Score 0.490 Round 5: 431 peptides, 59 chains. Longest chain 17 peptides. Score 0.547 Taking the results from Round 5 Chains 59, Residues 372, Estimated correctness of the model 0.0 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 12611 restraints for refining 5633 atoms. 11068 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2426 (Rfree = 0.000) for 5633 atoms. Found 26 (26 requested) and removed 78 (13 requested) atoms. Cycle 7: After refmac, R = 0.2177 (Rfree = 0.000) for 5498 atoms. Found 25 (26 requested) and removed 53 (13 requested) atoms. Cycle 8: After refmac, R = 0.1797 (Rfree = 0.000) for 5421 atoms. Found 16 (25 requested) and removed 27 (12 requested) atoms. Cycle 9: After refmac, R = 0.1843 (Rfree = 0.000) for 5386 atoms. Found 24 (25 requested) and removed 32 (12 requested) atoms. Cycle 10: After refmac, R = 0.1512 (Rfree = 0.000) for 5359 atoms. Found 9 (25 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.53 Search for helices and strands: 0 residues in 0 chains, 5534 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5549 seeds are put forward Round 1: 338 peptides, 62 chains. Longest chain 10 peptides. Score 0.361 Round 2: 395 peptides, 58 chains. Longest chain 18 peptides. Score 0.496 Round 3: 403 peptides, 59 chains. Longest chain 15 peptides. Score 0.503 Round 4: 425 peptides, 62 chains. Longest chain 25 peptides. Score 0.517 Round 5: 392 peptides, 55 chains. Longest chain 21 peptides. Score 0.514 Taking the results from Round 4 Chains 63, Residues 363, Estimated correctness of the model 0.0 % 6 chains (36 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 12690 restraints for refining 5733 atoms. 11168 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1992 (Rfree = 0.000) for 5733 atoms. Found 27 (27 requested) and removed 80 (13 requested) atoms. Cycle 12: After refmac, R = 0.1863 (Rfree = 0.000) for 5615 atoms. Found 26 (26 requested) and removed 57 (13 requested) atoms. Cycle 13: After refmac, R = 0.1773 (Rfree = 0.000) for 5554 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 14: After refmac, R = 0.1429 (Rfree = 0.000) for 5536 atoms. Found 14 (26 requested) and removed 23 (13 requested) atoms. Cycle 15: After refmac, R = 0.1335 (Rfree = 0.000) for 5503 atoms. Found 12 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.54 Search for helices and strands: 0 residues in 0 chains, 5660 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 5688 seeds are put forward Round 1: 339 peptides, 62 chains. Longest chain 14 peptides. Score 0.363 Round 2: 398 peptides, 66 chains. Longest chain 12 peptides. Score 0.441 Round 3: 433 peptides, 65 chains. Longest chain 17 peptides. Score 0.509 Round 4: 412 peptides, 65 chains. Longest chain 14 peptides. Score 0.473 Round 5: 396 peptides, 56 chains. Longest chain 22 peptides. Score 0.513 Taking the results from Round 5 Chains 59, Residues 340, Estimated correctness of the model 0.0 % 8 chains (53 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 13049 restraints for refining 5936 atoms. 11567 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1991 (Rfree = 0.000) for 5936 atoms. Found 28 (28 requested) and removed 54 (14 requested) atoms. Cycle 17: After refmac, R = 0.1794 (Rfree = 0.000) for 5844 atoms. Found 28 (28 requested) and removed 45 (14 requested) atoms. Cycle 18: After refmac, R = 0.1654 (Rfree = 0.000) for 5786 atoms. Found 22 (27 requested) and removed 30 (13 requested) atoms. Cycle 19: After refmac, R = 0.1582 (Rfree = 0.000) for 5755 atoms. Found 22 (27 requested) and removed 25 (13 requested) atoms. Cycle 20: After refmac, R = 0.1505 (Rfree = 0.000) for 5735 atoms. Found 15 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.53 Search for helices and strands: 0 residues in 0 chains, 5878 seeds are put forward NCS extension: 37 residues added (2 deleted due to clashes), 5915 seeds are put forward Round 1: 317 peptides, 62 chains. Longest chain 12 peptides. Score 0.319 Round 2: 356 peptides, 59 chains. Longest chain 13 peptides. Score 0.420 Round 3: 356 peptides, 55 chains. Longest chain 14 peptides. Score 0.452 Round 4: 367 peptides, 57 chains. Longest chain 13 peptides. Score 0.456 Round 5: 376 peptides, 58 chains. Longest chain 18 peptides. Score 0.464 Taking the results from Round 5 Chains 58, Residues 318, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 13481 restraints for refining 5902 atoms. 12230 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1929 (Rfree = 0.000) for 5902 atoms. Found 28 (28 requested) and removed 50 (14 requested) atoms. Cycle 22: After refmac, R = 0.1706 (Rfree = 0.000) for 5815 atoms. Found 18 (27 requested) and removed 37 (13 requested) atoms. Cycle 23: After refmac, R = 0.1614 (Rfree = 0.000) for 5767 atoms. Found 12 (27 requested) and removed 23 (13 requested) atoms. Cycle 24: After refmac, R = 0.1584 (Rfree = 0.000) for 5743 atoms. Found 22 (27 requested) and removed 23 (13 requested) atoms. Cycle 25: After refmac, R = 0.1637 (Rfree = 0.000) for 5734 atoms. Found 22 (27 requested) and removed 25 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.68 Search for helices and strands: 0 residues in 0 chains, 5888 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5902 seeds are put forward Round 1: 300 peptides, 62 chains. Longest chain 9 peptides. Score 0.283 Round 2: 365 peptides, 63 chains. Longest chain 14 peptides. Score 0.404 Round 3: 374 peptides, 62 chains. Longest chain 18 peptides. Score 0.429 Round 4: 369 peptides, 61 chains. Longest chain 17 peptides. Score 0.428 Round 5: 381 peptides, 59 chains. Longest chain 13 peptides. Score 0.465 Taking the results from Round 5 Chains 60, Residues 322, Estimated correctness of the model 0.0 % 8 chains (47 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 13354 restraints for refining 5953 atoms. 11988 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2037 (Rfree = 0.000) for 5953 atoms. Found 24 (28 requested) and removed 59 (14 requested) atoms. Cycle 27: After refmac, R = 0.2065 (Rfree = 0.000) for 5856 atoms. Found 28 (28 requested) and removed 45 (14 requested) atoms. Cycle 28: After refmac, R = 0.2047 (Rfree = 0.000) for 5808 atoms. Found 27 (27 requested) and removed 40 (13 requested) atoms. Cycle 29: After refmac, R = 0.1571 (Rfree = 0.000) for 5761 atoms. Found 17 (27 requested) and removed 37 (13 requested) atoms. Cycle 30: After refmac, R = 0.1457 (Rfree = 0.000) for 5722 atoms. Found 10 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.55 Search for helices and strands: 0 residues in 0 chains, 5870 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5887 seeds are put forward Round 1: 266 peptides, 56 chains. Longest chain 8 peptides. Score 0.264 Round 2: 343 peptides, 60 chains. Longest chain 16 peptides. Score 0.387 Round 3: 337 peptides, 58 chains. Longest chain 11 peptides. Score 0.392 Round 4: 322 peptides, 54 chains. Longest chain 16 peptides. Score 0.397 Round 5: 325 peptides, 54 chains. Longest chain 13 peptides. Score 0.402 Taking the results from Round 5 Chains 54, Residues 271, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 13441 restraints for refining 5837 atoms. 12384 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2022 (Rfree = 0.000) for 5837 atoms. Found 27 (27 requested) and removed 53 (13 requested) atoms. Cycle 32: After refmac, R = 0.1814 (Rfree = 0.000) for 5775 atoms. Found 21 (27 requested) and removed 41 (13 requested) atoms. Cycle 33: After refmac, R = 0.1764 (Rfree = 0.000) for 5734 atoms. Found 18 (27 requested) and removed 24 (13 requested) atoms. Cycle 34: After refmac, R = 0.1561 (Rfree = 0.000) for 5714 atoms. Found 8 (27 requested) and removed 20 (13 requested) atoms. Cycle 35: After refmac, R = 0.1837 (Rfree = 0.000) for 5692 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 3.59 Search for helices and strands: 0 residues in 0 chains, 5833 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 5855 seeds are put forward Round 1: 266 peptides, 58 chains. Longest chain 8 peptides. Score 0.245 Round 2: 322 peptides, 58 chains. Longest chain 14 peptides. Score 0.363 Round 3: 330 peptides, 58 chains. Longest chain 13 peptides. Score 0.379 Round 4: 346 peptides, 54 chains. Longest chain 13 peptides. Score 0.442 Round 5: 321 peptides, 49 chains. Longest chain 13 peptides. Score 0.436 Taking the results from Round 4 Chains 55, Residues 292, Estimated correctness of the model 0.0 % 5 chains (34 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 13010 restraints for refining 5831 atoms. 11792 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1997 (Rfree = 0.000) for 5831 atoms. Found 20 (27 requested) and removed 48 (13 requested) atoms. Cycle 37: After refmac, R = 0.1718 (Rfree = 0.000) for 5758 atoms. Found 17 (27 requested) and removed 30 (13 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1580 (Rfree = 0.000) for 5722 atoms. Found 10 (27 requested) and removed 20 (13 requested) atoms. Cycle 39: After refmac, R = 0.1546 (Rfree = 0.000) for 5701 atoms. Found 6 (27 requested) and removed 23 (13 requested) atoms. Cycle 40: After refmac, R = 0.1527 (Rfree = 0.000) for 5675 atoms. Found 10 (26 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.56 Search for helices and strands: 0 residues in 0 chains, 5811 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5825 seeds are put forward Round 1: 240 peptides, 49 chains. Longest chain 10 peptides. Score 0.271 Round 2: 294 peptides, 51 chains. Longest chain 17 peptides. Score 0.367 Round 3: 273 peptides, 50 chains. Longest chain 10 peptides. Score 0.333 Round 4: 295 peptides, 53 chains. Longest chain 12 peptides. Score 0.352 Round 5: 280 peptides, 47 chains. Longest chain 11 peptides. Score 0.374 Taking the results from Round 5 Chains 47, Residues 233, Estimated correctness of the model 0.0 % 6 chains (29 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 13291 restraints for refining 5770 atoms. 12335 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1975 (Rfree = 0.000) for 5770 atoms. Found 24 (27 requested) and removed 48 (13 requested) atoms. Cycle 42: After refmac, R = 0.1912 (Rfree = 0.000) for 5709 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. Cycle 43: After refmac, R = 0.1764 (Rfree = 0.000) for 5673 atoms. Found 21 (27 requested) and removed 24 (13 requested) atoms. Cycle 44: After refmac, R = 0.1684 (Rfree = 0.000) for 5647 atoms. Found 17 (26 requested) and removed 25 (13 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1533 (Rfree = 0.000) for 5623 atoms. Found 10 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 3.57 Search for helices and strands: 0 residues in 0 chains, 5746 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 5758 seeds are put forward Round 1: 237 peptides, 53 chains. Longest chain 8 peptides. Score 0.227 Round 2: 267 peptides, 50 chains. Longest chain 11 peptides. Score 0.321 Round 3: 263 peptides, 49 chains. Longest chain 11 peptides. Score 0.321 Round 4: 287 peptides, 52 chains. Longest chain 13 peptides. Score 0.344 Round 5: 305 peptides, 54 chains. Longest chain 11 peptides. Score 0.363 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 55, Residues 251, Estimated correctness of the model 0.0 % 9 chains (45 residues) have been docked in sequence Sequence coverage is 17 % Consider running further cycles of model building using 1vkz-4_warpNtrace.pdb as input Building loops using Loopy2018 55 chains (251 residues) following loop building 9 chains (45 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6916 reflections ( 96.32 % complete ) and 12500 restraints for refining 5656 atoms. 11415 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2056 (Rfree = 0.000) for 5656 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1785 (Rfree = 0.000) for 5593 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1828 (Rfree = 0.000) for 5553 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1656 (Rfree = 0.000) for 5523 atoms. TimeTaking 62.23