Sun 23 Dec 22:22:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1ztc-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1ztc-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1ztc-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1ztc-3.6-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1ztc-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1ztc-3.6-parrot-hancs ############### 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 22:22:56 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/hancs/ArpWArp/wArpResults/WorkingDir/1ztc-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1ztc-3.6-parrot-hancs/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 1117 and 0 Target number of residues in the AU: 1117 Target solvent content: 0.6527 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-3.6-parrot-hancs.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-3.6-parrot-hancs.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 3.600 Wilson plot Bfac: 79.77 20576 reflections ( 98.68 % complete ) and 0 restraints for refining 7835 atoms. Observations/parameters ratio is 0.66 ------------------------------------------------------ Starting model: R = 0.3328 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3073 (Rfree = 0.000) for 7835 atoms. Found 50 (50 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 2.52 Search for helices and strands: 0 residues in 0 chains, 8028 seeds are put forward NCS extension: 0 residues added, 8028 seeds are put forward Round 1: 585 peptides, 75 chains. Longest chain 20 peptides. Score 0.473 Round 2: 676 peptides, 63 chains. Longest chain 35 peptides. Score 0.592 Round 3: 682 peptides, 60 chains. Longest chain 57 peptides. Score 0.606 Round 4: 660 peptides, 53 chains. Longest chain 32 peptides. Score 0.615 Round 5: 668 peptides, 50 chains. Longest chain 41 peptides. Score 0.631 Taking the results from Round 5 Chains 54, Residues 618, Estimated correctness of the model 26.4 % 5 chains (111 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 12357 restraints for refining 6494 atoms. 9441 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2759 (Rfree = 0.000) for 6494 atoms. Found 41 (41 requested) and removed 49 (20 requested) atoms. Cycle 2: After refmac, R = 0.2587 (Rfree = 0.000) for 6396 atoms. Found 41 (41 requested) and removed 43 (20 requested) atoms. Cycle 3: After refmac, R = 0.2493 (Rfree = 0.000) for 6361 atoms. Found 41 (41 requested) and removed 32 (20 requested) atoms. Cycle 4: After refmac, R = 0.2402 (Rfree = 0.000) for 6352 atoms. Found 40 (40 requested) and removed 51 (20 requested) atoms. Cycle 5: After refmac, R = 0.2326 (Rfree = 0.000) for 6333 atoms. Found 29 (40 requested) and removed 28 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 2.54 Search for helices and strands: 0 residues in 0 chains, 6554 seeds are put forward NCS extension: 17 residues added (11 deleted due to clashes), 6571 seeds are put forward Round 1: 636 peptides, 64 chains. Longest chain 33 peptides. Score 0.558 Round 2: 651 peptides, 54 chains. Longest chain 34 peptides. Score 0.605 Round 3: 662 peptides, 58 chains. Longest chain 46 peptides. Score 0.599 Round 4: 679 peptides, 49 chains. Longest chain 50 peptides. Score 0.642 Round 5: 678 peptides, 55 chains. Longest chain 51 peptides. Score 0.621 Taking the results from Round 4 Chains 54, Residues 630, Estimated correctness of the model 30.3 % 5 chains (120 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 20576 reflections ( 98.68 % complete ) and 12018 restraints for refining 6409 atoms. 9021 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2794 (Rfree = 0.000) for 6409 atoms. Found 41 (41 requested) and removed 41 (20 requested) atoms. Cycle 7: After refmac, R = 0.2645 (Rfree = 0.000) for 6355 atoms. Found 41 (41 requested) and removed 29 (20 requested) atoms. Cycle 8: After refmac, R = 0.2624 (Rfree = 0.000) for 6339 atoms. Found 40 (40 requested) and removed 29 (20 requested) atoms. Cycle 9: After refmac, R = 0.2551 (Rfree = 0.000) for 6334 atoms. Found 40 (40 requested) and removed 28 (20 requested) atoms. Cycle 10: After refmac, R = 0.2587 (Rfree = 0.000) for 6326 atoms. Found 40 (40 requested) and removed 33 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 2.53 Search for helices and strands: 0 residues in 0 chains, 6552 seeds are put forward NCS extension: 16 residues added (16 deleted due to clashes), 6568 seeds are put forward Round 1: 644 peptides, 55 chains. Longest chain 45 peptides. Score 0.597 Round 2: 673 peptides, 55 chains. Longest chain 38 peptides. Score 0.617 Round 3: 670 peptides, 53 chains. Longest chain 39 peptides. Score 0.622 Round 4: 666 peptides, 54 chains. Longest chain 40 peptides. Score 0.616 Round 5: 700 peptides, 47 chains. Longest chain 60 peptides. Score 0.662 Taking the results from Round 5 Chains 49, Residues 653, Estimated correctness of the model 37.3 % 6 chains (207 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 11062 restraints for refining 6408 atoms. 7594 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2850 (Rfree = 0.000) for 6408 atoms. Found 41 (41 requested) and removed 50 (20 requested) atoms. Cycle 12: After refmac, R = 0.2695 (Rfree = 0.000) for 6343 atoms. Found 40 (41 requested) and removed 37 (20 requested) atoms. Cycle 13: After refmac, R = 0.2597 (Rfree = 0.000) for 6321 atoms. Found 40 (40 requested) and removed 32 (20 requested) atoms. Cycle 14: After refmac, R = 0.2548 (Rfree = 0.000) for 6321 atoms. Found 11 (40 requested) and removed 25 (20 requested) atoms. Cycle 15: After refmac, R = 0.2558 (Rfree = 0.000) for 6293 atoms. Found 20 (40 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 2.53 Search for helices and strands: 0 residues in 0 chains, 6507 seeds are put forward NCS extension: 25 residues added (19 deleted due to clashes), 6532 seeds are put forward Round 1: 637 peptides, 62 chains. Longest chain 39 peptides. Score 0.566 Round 2: 665 peptides, 55 chains. Longest chain 42 peptides. Score 0.612 Round 3: 674 peptides, 58 chains. Longest chain 48 peptides. Score 0.608 Round 4: 660 peptides, 56 chains. Longest chain 44 peptides. Score 0.605 Round 5: 658 peptides, 56 chains. Longest chain 42 peptides. Score 0.603 Taking the results from Round 2 Chains 60, Residues 610, Estimated correctness of the model 19.3 % 5 chains (124 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 12213 restraints for refining 6411 atoms. 9304 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2758 (Rfree = 0.000) for 6411 atoms. Found 41 (41 requested) and removed 43 (20 requested) atoms. Cycle 17: After refmac, R = 0.2552 (Rfree = 0.000) for 6365 atoms. Found 40 (41 requested) and removed 35 (20 requested) atoms. Cycle 18: After refmac, R = 0.2488 (Rfree = 0.000) for 6351 atoms. Found 30 (40 requested) and removed 40 (20 requested) atoms. Cycle 19: After refmac, R = 0.2470 (Rfree = 0.000) for 6333 atoms. Found 20 (40 requested) and removed 27 (20 requested) atoms. Cycle 20: After refmac, R = 0.2439 (Rfree = 0.000) for 6318 atoms. Found 16 (40 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 2.54 Search for helices and strands: 0 residues in 0 chains, 6484 seeds are put forward NCS extension: 29 residues added (13 deleted due to clashes), 6513 seeds are put forward Round 1: 607 peptides, 58 chains. Longest chain 38 peptides. Score 0.558 Round 2: 635 peptides, 57 chains. Longest chain 41 peptides. Score 0.583 Round 3: 648 peptides, 61 chains. Longest chain 33 peptides. Score 0.578 Round 4: 657 peptides, 58 chains. Longest chain 44 peptides. Score 0.596 Round 5: 631 peptides, 61 chains. Longest chain 33 peptides. Score 0.565 Taking the results from Round 4 Chains 59, Residues 599, Estimated correctness of the model 13.1 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 13477 restraints for refining 6411 atoms. 11044 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2740 (Rfree = 0.000) for 6411 atoms. Found 41 (41 requested) and removed 23 (20 requested) atoms. Cycle 22: After refmac, R = 0.2509 (Rfree = 0.000) for 6403 atoms. Found 36 (41 requested) and removed 26 (20 requested) atoms. Cycle 23: After refmac, R = 0.2450 (Rfree = 0.000) for 6399 atoms. Found 25 (41 requested) and removed 22 (20 requested) atoms. Cycle 24: After refmac, R = 0.2418 (Rfree = 0.000) for 6395 atoms. Found 22 (41 requested) and removed 20 (20 requested) atoms. Cycle 25: After refmac, R = 0.2400 (Rfree = 0.000) for 6391 atoms. Found 23 (41 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 2.55 Search for helices and strands: 0 residues in 0 chains, 6605 seeds are put forward NCS extension: 30 residues added (26 deleted due to clashes), 6635 seeds are put forward Round 1: 618 peptides, 65 chains. Longest chain 46 peptides. Score 0.540 Round 2: 647 peptides, 57 chains. Longest chain 36 peptides. Score 0.592 Round 3: 663 peptides, 54 chains. Longest chain 34 peptides. Score 0.614 Round 4: 633 peptides, 58 chains. Longest chain 33 peptides. Score 0.578 Round 5: 648 peptides, 55 chains. Longest chain 50 peptides. Score 0.600 Taking the results from Round 3 Chains 56, Residues 609, Estimated correctness of the model 20.0 % 3 chains (34 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 13130 restraints for refining 6411 atoms. 10612 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2717 (Rfree = 0.000) for 6411 atoms. Found 41 (41 requested) and removed 32 (20 requested) atoms. Cycle 27: After refmac, R = 0.2490 (Rfree = 0.000) for 6384 atoms. Found 34 (41 requested) and removed 30 (20 requested) atoms. Cycle 28: After refmac, R = 0.2418 (Rfree = 0.000) for 6367 atoms. Found 26 (40 requested) and removed 25 (20 requested) atoms. Cycle 29: After refmac, R = 0.2398 (Rfree = 0.000) for 6357 atoms. Found 27 (40 requested) and removed 30 (20 requested) atoms. Cycle 30: After refmac, R = 0.2320 (Rfree = 0.000) for 6345 atoms. Found 17 (40 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 2.56 Search for helices and strands: 0 residues in 0 chains, 6531 seeds are put forward NCS extension: 25 residues added (28 deleted due to clashes), 6556 seeds are put forward Round 1: 610 peptides, 66 chains. Longest chain 35 peptides. Score 0.530 Round 2: 649 peptides, 59 chains. Longest chain 40 peptides. Score 0.586 Round 3: 632 peptides, 63 chains. Longest chain 30 peptides. Score 0.559 Round 4: 646 peptides, 58 chains. Longest chain 34 peptides. Score 0.588 Round 5: 645 peptides, 60 chains. Longest chain 48 peptides. Score 0.580 Taking the results from Round 4 Chains 59, Residues 588, Estimated correctness of the model 9.9 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 13615 restraints for refining 6411 atoms. 11267 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2764 (Rfree = 0.000) for 6411 atoms. Found 41 (41 requested) and removed 29 (20 requested) atoms. Cycle 32: After refmac, R = 0.2511 (Rfree = 0.000) for 6392 atoms. Found 41 (41 requested) and removed 22 (20 requested) atoms. Cycle 33: After refmac, R = 0.2439 (Rfree = 0.000) for 6391 atoms. Found 35 (41 requested) and removed 26 (20 requested) atoms. Cycle 34: After refmac, R = 0.2336 (Rfree = 0.000) for 6383 atoms. Found 26 (41 requested) and removed 20 (20 requested) atoms. Cycle 35: After refmac, R = 0.2312 (Rfree = 0.000) for 6381 atoms. Found 32 (40 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 2.52 Search for helices and strands: 0 residues in 0 chains, 6615 seeds are put forward NCS extension: 20 residues added (10 deleted due to clashes), 6635 seeds are put forward Round 1: 598 peptides, 68 chains. Longest chain 24 peptides. Score 0.512 Round 2: 655 peptides, 58 chains. Longest chain 42 peptides. Score 0.594 Round 3: 634 peptides, 53 chains. Longest chain 50 peptides. Score 0.597 Round 4: 623 peptides, 55 chains. Longest chain 36 peptides. Score 0.581 Round 5: 621 peptides, 57 chains. Longest chain 29 peptides. Score 0.573 Taking the results from Round 3 Chains 53, Residues 581, Estimated correctness of the model 13.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 13853 restraints for refining 6410 atoms. 11582 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2572 (Rfree = 0.000) for 6410 atoms. Found 41 (41 requested) and removed 25 (20 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2312 (Rfree = 0.000) for 6392 atoms. Found 26 (41 requested) and removed 33 (20 requested) atoms. Cycle 38: After refmac, R = 0.2268 (Rfree = 0.000) for 6369 atoms. Found 22 (40 requested) and removed 23 (20 requested) atoms. Cycle 39: After refmac, R = 0.2198 (Rfree = 0.000) for 6356 atoms. Found 24 (40 requested) and removed 23 (20 requested) atoms. Cycle 40: After refmac, R = 0.2191 (Rfree = 0.000) for 6352 atoms. Found 14 (40 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 2.53 Search for helices and strands: 0 residues in 0 chains, 6585 seeds are put forward NCS extension: 39 residues added (13 deleted due to clashes), 6624 seeds are put forward Round 1: 607 peptides, 72 chains. Longest chain 33 peptides. Score 0.504 Round 2: 652 peptides, 61 chains. Longest chain 34 peptides. Score 0.581 Round 3: 664 peptides, 61 chains. Longest chain 31 peptides. Score 0.590 Round 4: 641 peptides, 63 chains. Longest chain 38 peptides. Score 0.566 Round 5: 646 peptides, 56 chains. Longest chain 34 peptides. Score 0.595 Taking the results from Round 5 Chains 59, Residues 590, Estimated correctness of the model 12.7 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 20576 reflections ( 98.68 % complete ) and 13355 restraints for refining 6408 atoms. 10907 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2627 (Rfree = 0.000) for 6408 atoms. Found 41 (41 requested) and removed 34 (20 requested) atoms. Cycle 42: After refmac, R = 0.2373 (Rfree = 0.000) for 6376 atoms. Found 18 (41 requested) and removed 26 (20 requested) atoms. Cycle 43: After refmac, R = 0.2304 (Rfree = 0.000) for 6349 atoms. Found 30 (40 requested) and removed 24 (20 requested) atoms. Cycle 44: After refmac, R = 0.2265 (Rfree = 0.000) for 6349 atoms. Found 15 (40 requested) and removed 30 (20 requested) atoms. Cycle 45: After refmac, R = 0.2213 (Rfree = 0.000) for 6326 atoms. Found 26 (40 requested) and removed 28 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 2.53 Search for helices and strands: 0 residues in 0 chains, 6524 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 6556 seeds are put forward Round 1: 615 peptides, 73 chains. Longest chain 27 peptides. Score 0.507 Round 2: 639 peptides, 59 chains. Longest chain 26 peptides. Score 0.579 Round 3: 622 peptides, 60 chains. Longest chain 37 peptides. Score 0.562 Round 4: 633 peptides, 55 chains. Longest chain 42 peptides. Score 0.589 Round 5: 625 peptides, 60 chains. Longest chain 30 peptides. Score 0.564 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 578, Estimated correctness of the model 10.3 % 4 chains (70 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 1ztc-3_warpNtrace.pdb as input Building loops using Loopy2018 57 chains (578 residues) following loop building 4 chains (70 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20576 reflections ( 98.68 % complete ) and 13115 restraints for refining 6409 atoms. 10538 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2607 (Rfree = 0.000) for 6409 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.2428 (Rfree = 0.000) for 6357 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2368 (Rfree = 0.000) for 6331 atoms. Found 0 (40 requested) and removed 16 (20 requested) atoms. Cycle 49: After refmac, R = 0.2337 (Rfree = 0.000) for 6304 atoms. TimeTaking 97.92