Mon 24 Dec 07:34:25 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vr0-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vr0-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vr0-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.2-parrot-noncs ############### 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 07:34:29 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/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.2-parrot-noncs/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 523 and 0 Target number of residues in the AU: 523 Target solvent content: 0.6136 Checking the provided sequence file Detected sequence length: 247 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 741 Adjusted target solvent content: 0.45 Input MTZ file: 1vr0-3.2-parrot-noncs.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: 20 Cell parameters: 46.686 69.193 453.518 90.000 90.000 90.000 Input sequence file: 1vr0-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 5928 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: 226.759 3.200 Wilson plot Bfac: 58.25 12698 reflections ( 99.73 % complete ) and 0 restraints for refining 6575 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3152 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2587 (Rfree = 0.000) for 6575 atoms. Found 41 (59 requested) and removed 72 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.09 3.30 Search for helices and strands: 0 residues in 0 chains, 6699 seeds are put forward NCS extension: 0 residues added, 6699 seeds are put forward Round 1: 333 peptides, 63 chains. Longest chain 13 peptides. Score 0.363 Round 2: 422 peptides, 66 chains. Longest chain 17 peptides. Score 0.518 Round 3: 439 peptides, 66 chains. Longest chain 23 peptides. Score 0.548 Round 4: 461 peptides, 63 chains. Longest chain 25 peptides. Score 0.607 Round 5: 454 peptides, 58 chains. Longest chain 26 peptides. Score 0.630 Taking the results from Round 5 Chains 59, Residues 396, Estimated correctness of the model 48.9 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11928 restraints for refining 5408 atoms. 10340 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2613 (Rfree = 0.000) for 5408 atoms. Found 30 (48 requested) and removed 49 (24 requested) atoms. Cycle 2: After refmac, R = 0.2639 (Rfree = 0.000) for 5329 atoms. Found 21 (48 requested) and removed 46 (24 requested) atoms. Cycle 3: After refmac, R = 0.2639 (Rfree = 0.000) for 5277 atoms. Found 38 (47 requested) and removed 40 (23 requested) atoms. Cycle 4: After refmac, R = 0.2387 (Rfree = 0.000) for 5261 atoms. Found 27 (47 requested) and removed 36 (23 requested) atoms. Cycle 5: After refmac, R = 0.2127 (Rfree = 0.000) for 5242 atoms. Found 17 (47 requested) and removed 28 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.07 3.28 Search for helices and strands: 0 residues in 0 chains, 5424 seeds are put forward NCS extension: 17 residues added (14 deleted due to clashes), 5441 seeds are put forward Round 1: 401 peptides, 65 chains. Longest chain 21 peptides. Score 0.487 Round 2: 432 peptides, 54 chains. Longest chain 25 peptides. Score 0.624 Round 3: 446 peptides, 53 chains. Longest chain 25 peptides. Score 0.652 Round 4: 436 peptides, 48 chains. Longest chain 30 peptides. Score 0.670 Round 5: 448 peptides, 48 chains. Longest chain 50 peptides. Score 0.686 Taking the results from Round 5 Chains 50, Residues 400, Estimated correctness of the model 62.2 % 5 chains (97 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11014 restraints for refining 5412 atoms. 9099 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2402 (Rfree = 0.000) for 5412 atoms. Found 36 (48 requested) and removed 47 (24 requested) atoms. Cycle 7: After refmac, R = 0.2237 (Rfree = 0.000) for 5378 atoms. Found 14 (48 requested) and removed 37 (24 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2210 (Rfree = 0.000) for 5348 atoms. Found 13 (48 requested) and removed 38 (24 requested) atoms. Cycle 9: After refmac, R = 0.2516 (Rfree = 0.000) for 5321 atoms. Found 47 (47 requested) and removed 47 (23 requested) atoms. Cycle 10: After refmac, R = 0.2230 (Rfree = 0.000) for 5310 atoms. Found 11 (47 requested) and removed 30 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 3.29 Search for helices and strands: 0 residues in 0 chains, 5488 seeds are put forward NCS extension: 31 residues added (5 deleted due to clashes), 5519 seeds are put forward Round 1: 394 peptides, 54 chains. Longest chain 23 peptides. Score 0.562 Round 2: 438 peptides, 48 chains. Longest chain 30 peptides. Score 0.673 Round 3: 453 peptides, 55 chains. Longest chain 36 peptides. Score 0.649 Round 4: 454 peptides, 52 chains. Longest chain 31 peptides. Score 0.669 Round 5: 443 peptides, 51 chains. Longest chain 32 peptides. Score 0.660 Taking the results from Round 2 Chains 51, Residues 390, Estimated correctness of the model 59.2 % 3 chains (71 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11287 restraints for refining 5412 atoms. 9498 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2228 (Rfree = 0.000) for 5412 atoms. Found 27 (48 requested) and removed 38 (24 requested) atoms. Cycle 12: After refmac, R = 0.2289 (Rfree = 0.000) for 5385 atoms. Found 12 (48 requested) and removed 29 (24 requested) atoms. Cycle 13: After refmac, R = 0.2106 (Rfree = 0.000) for 5364 atoms. Found 12 (48 requested) and removed 26 (24 requested) atoms. Cycle 14: After refmac, R = 0.2353 (Rfree = 0.000) for 5335 atoms. Found 46 (48 requested) and removed 31 (24 requested) atoms. Cycle 15: After refmac, R = 0.1970 (Rfree = 0.000) for 5340 atoms. Found 19 (48 requested) and removed 31 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.05 3.26 Search for helices and strands: 0 residues in 0 chains, 5503 seeds are put forward NCS extension: 31 residues added (7 deleted due to clashes), 5534 seeds are put forward Round 1: 390 peptides, 54 chains. Longest chain 31 peptides. Score 0.555 Round 2: 419 peptides, 48 chains. Longest chain 28 peptides. Score 0.646 Round 3: 445 peptides, 56 chains. Longest chain 28 peptides. Score 0.630 Round 4: 454 peptides, 49 chains. Longest chain 28 peptides. Score 0.688 Round 5: 423 peptides, 46 chains. Longest chain 32 peptides. Score 0.665 Taking the results from Round 4 Chains 52, Residues 405, Estimated correctness of the model 62.6 % 5 chains (81 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11156 restraints for refining 5412 atoms. 9306 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2169 (Rfree = 0.000) for 5412 atoms. Found 18 (48 requested) and removed 35 (24 requested) atoms. Cycle 17: After refmac, R = 0.2016 (Rfree = 0.000) for 5384 atoms. Found 17 (48 requested) and removed 24 (24 requested) atoms. Cycle 18: After refmac, R = 0.1920 (Rfree = 0.000) for 5373 atoms. Found 12 (48 requested) and removed 29 (24 requested) atoms. Cycle 19: After refmac, R = 0.1912 (Rfree = 0.000) for 5348 atoms. Found 9 (48 requested) and removed 29 (24 requested) atoms. Cycle 20: After refmac, R = 0.1889 (Rfree = 0.000) for 5323 atoms. Found 9 (47 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.04 3.25 Search for helices and strands: 0 residues in 0 chains, 5507 seeds are put forward NCS extension: 32 residues added (13 deleted due to clashes), 5539 seeds are put forward Round 1: 407 peptides, 56 chains. Longest chain 21 peptides. Score 0.569 Round 2: 430 peptides, 47 chains. Longest chain 41 peptides. Score 0.668 Round 3: 431 peptides, 46 chains. Longest chain 28 peptides. Score 0.676 Round 4: 437 peptides, 48 chains. Longest chain 28 peptides. Score 0.671 Round 5: 427 peptides, 46 chains. Longest chain 42 peptides. Score 0.670 Taking the results from Round 3 Chains 49, Residues 385, Estimated correctness of the model 59.9 % 6 chains (90 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11194 restraints for refining 5412 atoms. 9361 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2143 (Rfree = 0.000) for 5412 atoms. Found 24 (48 requested) and removed 43 (24 requested) atoms. Cycle 22: After refmac, R = 0.2496 (Rfree = 0.000) for 5386 atoms. Found 40 (48 requested) and removed 39 (24 requested) atoms. Cycle 23: After refmac, R = 0.2330 (Rfree = 0.000) for 5375 atoms. Found 38 (48 requested) and removed 33 (24 requested) atoms. Cycle 24: After refmac, R = 0.1777 (Rfree = 0.000) for 5374 atoms. Found 12 (48 requested) and removed 27 (24 requested) atoms. Cycle 25: After refmac, R = 0.1730 (Rfree = 0.000) for 5354 atoms. Found 5 (48 requested) and removed 31 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.04 3.25 Search for helices and strands: 0 residues in 0 chains, 5519 seeds are put forward NCS extension: 21 residues added (9 deleted due to clashes), 5540 seeds are put forward Round 1: 384 peptides, 57 chains. Longest chain 28 peptides. Score 0.520 Round 2: 438 peptides, 56 chains. Longest chain 29 peptides. Score 0.619 Round 3: 415 peptides, 54 chains. Longest chain 21 peptides. Score 0.597 Round 4: 429 peptides, 57 chains. Longest chain 24 peptides. Score 0.598 Round 5: 430 peptides, 57 chains. Longest chain 30 peptides. Score 0.600 Taking the results from Round 2 Chains 60, Residues 382, Estimated correctness of the model 46.1 % 4 chains (69 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11153 restraints for refining 5411 atoms. 9425 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2025 (Rfree = 0.000) for 5411 atoms. Found 21 (48 requested) and removed 42 (24 requested) atoms. Cycle 27: After refmac, R = 0.1942 (Rfree = 0.000) for 5380 atoms. Found 18 (48 requested) and removed 24 (24 requested) atoms. Cycle 28: After refmac, R = 0.1917 (Rfree = 0.000) for 5374 atoms. Found 5 (48 requested) and removed 27 (24 requested) atoms. Cycle 29: After refmac, R = 0.1878 (Rfree = 0.000) for 5348 atoms. Found 3 (48 requested) and removed 26 (24 requested) atoms. Cycle 30: After refmac, R = 0.1896 (Rfree = 0.000) for 5322 atoms. Found 6 (47 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.06 3.27 Search for helices and strands: 0 residues in 0 chains, 5483 seeds are put forward NCS extension: 56 residues added (5 deleted due to clashes), 5539 seeds are put forward Round 1: 359 peptides, 55 chains. Longest chain 18 peptides. Score 0.489 Round 2: 394 peptides, 50 chains. Longest chain 29 peptides. Score 0.592 Round 3: 387 peptides, 54 chains. Longest chain 20 peptides. Score 0.549 Round 4: 391 peptides, 54 chains. Longest chain 21 peptides. Score 0.557 Round 5: 382 peptides, 53 chains. Longest chain 27 peptides. Score 0.549 Taking the results from Round 2 Chains 53, Residues 344, Estimated correctness of the model 38.9 % 4 chains (72 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11448 restraints for refining 5412 atoms. 9869 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2042 (Rfree = 0.000) for 5412 atoms. Found 12 (48 requested) and removed 29 (24 requested) atoms. Cycle 32: After refmac, R = 0.1992 (Rfree = 0.000) for 5390 atoms. Found 6 (48 requested) and removed 24 (24 requested) atoms. Cycle 33: After refmac, R = 0.2063 (Rfree = 0.000) for 5369 atoms. Found 16 (48 requested) and removed 25 (24 requested) atoms. Cycle 34: After refmac, R = 0.2182 (Rfree = 0.000) for 5356 atoms. Found 24 (48 requested) and removed 28 (24 requested) atoms. Cycle 35: After refmac, R = 0.2062 (Rfree = 0.000) for 5350 atoms. Found 17 (48 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.06 3.27 Search for helices and strands: 0 residues in 0 chains, 5530 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 5555 seeds are put forward Round 1: 345 peptides, 53 chains. Longest chain 20 peptides. Score 0.479 Round 2: 385 peptides, 50 chains. Longest chain 23 peptides. Score 0.577 Round 3: 408 peptides, 55 chains. Longest chain 24 peptides. Score 0.578 Round 4: 373 peptides, 50 chains. Longest chain 21 peptides. Score 0.556 Round 5: 360 peptides, 48 chains. Longest chain 37 peptides. Score 0.549 Taking the results from Round 3 Chains 57, Residues 353, Estimated correctness of the model 35.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11842 restraints for refining 5412 atoms. 10383 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2038 (Rfree = 0.000) for 5412 atoms. Found 18 (48 requested) and removed 29 (24 requested) atoms. Cycle 37: After refmac, R = 0.1935 (Rfree = 0.000) for 5394 atoms. Found 6 (48 requested) and removed 24 (24 requested) atoms. Cycle 38: After refmac, R = 0.2177 (Rfree = 0.000) for 5372 atoms. Found 35 (48 requested) and removed 27 (24 requested) atoms. Cycle 39: After refmac, R = 0.2211 (Rfree = 0.000) for 5376 atoms. Found 39 (48 requested) and removed 30 (24 requested) atoms. Cycle 40: After refmac, R = 0.1837 (Rfree = 0.000) for 5380 atoms. Found 9 (48 requested) and removed 32 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.07 3.28 Search for helices and strands: 0 residues in 0 chains, 5510 seeds are put forward NCS extension: 37 residues added (2 deleted due to clashes), 5547 seeds are put forward Round 1: 358 peptides, 56 chains. Longest chain 41 peptides. Score 0.479 Round 2: 357 peptides, 47 chains. Longest chain 20 peptides. Score 0.552 Round 3: 368 peptides, 52 chains. Longest chain 41 peptides. Score 0.531 Round 4: 367 peptides, 49 chains. Longest chain 31 peptides. Score 0.554 Round 5: 377 peptides, 53 chains. Longest chain 23 peptides. Score 0.540 Taking the results from Round 4 Chains 49, Residues 318, Estimated correctness of the model 28.1 % 2 chains (47 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11900 restraints for refining 5412 atoms. 10511 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1998 (Rfree = 0.000) for 5412 atoms. Found 18 (48 requested) and removed 28 (24 requested) atoms. Cycle 42: After refmac, R = 0.1909 (Rfree = 0.000) for 5400 atoms. Found 7 (48 requested) and removed 25 (24 requested) atoms. Cycle 43: After refmac, R = 0.1895 (Rfree = 0.000) for 5379 atoms. Found 5 (48 requested) and removed 24 (24 requested) atoms. Cycle 44: After refmac, R = 0.1850 (Rfree = 0.000) for 5354 atoms. Found 13 (48 requested) and removed 24 (24 requested) atoms. Cycle 45: After refmac, R = 0.1780 (Rfree = 0.000) for 5339 atoms. Found 15 (47 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 3.30 Search for helices and strands: 0 residues in 0 chains, 5497 seeds are put forward NCS extension: 28 residues added (5 deleted due to clashes), 5525 seeds are put forward Round 1: 326 peptides, 54 chains. Longest chain 21 peptides. Score 0.431 Round 2: 353 peptides, 53 chains. Longest chain 21 peptides. Score 0.494 Round 3: 357 peptides, 51 chains. Longest chain 24 peptides. Score 0.519 Round 4: 352 peptides, 49 chains. Longest chain 19 peptides. Score 0.526 Round 5: 355 peptides, 50 chains. Longest chain 20 peptides. Score 0.524 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 303, Estimated correctness of the model 19.6 % 2 chains (20 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vr0-3_warpNtrace.pdb as input Building loops using Loopy2018 50 chains (303 residues) following loop building 2 chains (20 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12698 reflections ( 99.73 % complete ) and 12144 restraints for refining 5412 atoms. 10913 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1828 (Rfree = 0.000) for 5412 atoms. Found 0 (48 requested) and removed 19 (24 requested) atoms. Cycle 47: After refmac, R = 0.1782 (Rfree = 0.000) for 5387 atoms. Found 0 (48 requested) and removed 12 (24 requested) atoms. Cycle 48: After refmac, R = 0.1745 (Rfree = 0.000) for 5374 atoms. Found 0 (48 requested) and removed 10 (24 requested) atoms. Cycle 49: After refmac, R = 0.1848 (Rfree = 0.000) for 5361 atoms. TimeTaking 64.87