Mon 24 Dec 01:05:29 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 2it9-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2it9-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2it9-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2it9-3.4-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/2it9-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2it9-3.4-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 01:05:33 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/2it9-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2it9-3.4-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 403 and 0 Target number of residues in the AU: 403 Target solvent content: 0.6375 Checking the provided sequence file Detected sequence length: 127 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 508 Adjusted target solvent content: 0.54 Input MTZ file: 2it9-3.4-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: 59.723 81.014 124.347 90.000 90.000 90.000 Input sequence file: 2it9-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4064 target number of atoms Had to go as low as 0.85 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: 67.879 3.400 Wilson plot Bfac: 70.20 8621 reflections ( 98.45 % complete ) and 0 restraints for refining 4513 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3451 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2272 (Rfree = 0.000) for 4513 atoms. Found 28 (34 requested) and removed 30 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 4606 seeds are put forward NCS extension: 0 residues added, 4606 seeds are put forward Round 1: 275 peptides, 48 chains. Longest chain 14 peptides. Score 0.409 Round 2: 337 peptides, 43 chains. Longest chain 26 peptides. Score 0.601 Round 3: 335 peptides, 42 chains. Longest chain 23 peptides. Score 0.606 Round 4: 365 peptides, 38 chains. Longest chain 23 peptides. Score 0.692 Round 5: 360 peptides, 35 chains. Longest chain 22 peptides. Score 0.706 Taking the results from Round 5 Chains 35, Residues 325, Estimated correctness of the model 59.4 % 2 chains (24 residues) have been docked in sequence Building loops using Loopy2018 35 chains (325 residues) following loop building 2 chains (24 residues) in sequence following loop building ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 7608 restraints for refining 3693 atoms. 6248 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2977 (Rfree = 0.000) for 3693 atoms. Found 26 (27 requested) and removed 26 (13 requested) atoms. Cycle 2: After refmac, R = 0.2764 (Rfree = 0.000) for 3674 atoms. Found 22 (26 requested) and removed 21 (13 requested) atoms. Cycle 3: After refmac, R = 0.2639 (Rfree = 0.000) for 3656 atoms. Found 9 (26 requested) and removed 20 (13 requested) atoms. Cycle 4: After refmac, R = 0.2545 (Rfree = 0.000) for 3635 atoms. Found 6 (25 requested) and removed 14 (13 requested) atoms. Cycle 5: After refmac, R = 0.2520 (Rfree = 0.000) for 3616 atoms. Found 9 (25 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 3706 seeds are put forward NCS extension: 15 residues added (6 deleted due to clashes), 3721 seeds are put forward Round 1: 296 peptides, 40 chains. Longest chain 20 peptides. Score 0.544 Round 2: 370 peptides, 45 chains. Longest chain 20 peptides. Score 0.646 Round 3: 365 peptides, 41 chains. Longest chain 26 peptides. Score 0.669 Round 4: 361 peptides, 42 chains. Longest chain 27 peptides. Score 0.654 Round 5: 371 peptides, 41 chains. Longest chain 22 peptides. Score 0.679 Taking the results from Round 5 Chains 41, Residues 330, Estimated correctness of the model 52.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 7858 restraints for refining 3695 atoms. 6579 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2797 (Rfree = 0.000) for 3695 atoms. Found 24 (24 requested) and removed 24 (13 requested) atoms. Cycle 7: After refmac, R = 0.2647 (Rfree = 0.000) for 3687 atoms. Found 16 (24 requested) and removed 15 (13 requested) atoms. Cycle 8: After refmac, R = 0.2555 (Rfree = 0.000) for 3685 atoms. Found 6 (24 requested) and removed 13 (13 requested) atoms. Cycle 9: After refmac, R = 0.2508 (Rfree = 0.000) for 3675 atoms. Found 1 (24 requested) and removed 14 (13 requested) atoms. Cycle 10: After refmac, R = 0.2485 (Rfree = 0.000) for 3661 atoms. Found 2 (24 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.20 Search for helices and strands: 0 residues in 0 chains, 3750 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 3769 seeds are put forward Round 1: 293 peptides, 41 chains. Longest chain 19 peptides. Score 0.527 Round 2: 335 peptides, 47 chains. Longest chain 18 peptides. Score 0.561 Round 3: 340 peptides, 41 chains. Longest chain 19 peptides. Score 0.624 Round 4: 354 peptides, 43 chains. Longest chain 21 peptides. Score 0.634 Round 5: 345 peptides, 41 chains. Longest chain 21 peptides. Score 0.634 Taking the results from Round 5 Chains 42, Residues 304, Estimated correctness of the model 39.4 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 7904 restraints for refining 3694 atoms. 6685 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2992 (Rfree = 0.000) for 3694 atoms. Found 24 (24 requested) and removed 19 (13 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2805 (Rfree = 0.000) for 3696 atoms. Found 8 (24 requested) and removed 15 (13 requested) atoms. Cycle 13: After refmac, R = 0.2682 (Rfree = 0.000) for 3685 atoms. Found 3 (24 requested) and removed 13 (13 requested) atoms. Cycle 14: After refmac, R = 0.2613 (Rfree = 0.000) for 3670 atoms. Found 6 (24 requested) and removed 13 (13 requested) atoms. Cycle 15: After refmac, R = 0.2563 (Rfree = 0.000) for 3661 atoms. Found 2 (24 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 3756 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3768 seeds are put forward Round 1: 294 peptides, 47 chains. Longest chain 16 peptides. Score 0.468 Round 2: 344 peptides, 44 chains. Longest chain 18 peptides. Score 0.606 Round 3: 346 peptides, 44 chains. Longest chain 36 peptides. Score 0.610 Round 4: 338 peptides, 39 chains. Longest chain 21 peptides. Score 0.638 Round 5: 343 peptides, 41 chains. Longest chain 24 peptides. Score 0.630 Taking the results from Round 4 Chains 39, Residues 299, Estimated correctness of the model 40.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8121 restraints for refining 3695 atoms. 6964 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2638 (Rfree = 0.000) for 3695 atoms. Found 15 (24 requested) and removed 14 (13 requested) atoms. Cycle 17: After refmac, R = 0.2470 (Rfree = 0.000) for 3691 atoms. Found 6 (24 requested) and removed 13 (13 requested) atoms. Cycle 18: After refmac, R = 0.2453 (Rfree = 0.000) for 3683 atoms. Found 5 (24 requested) and removed 13 (13 requested) atoms. Cycle 19: After refmac, R = 0.2473 (Rfree = 0.000) for 3674 atoms. Found 2 (24 requested) and removed 13 (13 requested) atoms. Cycle 20: After refmac, R = 0.2510 (Rfree = 0.000) for 3660 atoms. Found 5 (24 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 3771 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 3794 seeds are put forward Round 1: 299 peptides, 47 chains. Longest chain 16 peptides. Score 0.480 Round 2: 308 peptides, 41 chains. Longest chain 23 peptides. Score 0.560 Round 3: 303 peptides, 39 chains. Longest chain 20 peptides. Score 0.569 Round 4: 319 peptides, 40 chains. Longest chain 20 peptides. Score 0.592 Round 5: 328 peptides, 41 chains. Longest chain 23 peptides. Score 0.601 Taking the results from Round 5 Chains 41, Residues 287, Estimated correctness of the model 29.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8214 restraints for refining 3695 atoms. 7107 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2634 (Rfree = 0.000) for 3695 atoms. Found 13 (24 requested) and removed 19 (13 requested) atoms. Cycle 22: After refmac, R = 0.2504 (Rfree = 0.000) for 3682 atoms. Found 10 (24 requested) and removed 16 (13 requested) atoms. Cycle 23: After refmac, R = 0.2401 (Rfree = 0.000) for 3671 atoms. Found 3 (24 requested) and removed 13 (13 requested) atoms. Cycle 24: After refmac, R = 0.2478 (Rfree = 0.000) for 3659 atoms. Found 12 (24 requested) and removed 15 (13 requested) atoms. Cycle 25: After refmac, R = 0.2394 (Rfree = 0.000) for 3651 atoms. Found 5 (24 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 3744 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 3772 seeds are put forward Round 1: 268 peptides, 41 chains. Longest chain 17 peptides. Score 0.468 Round 2: 307 peptides, 45 chains. Longest chain 19 peptides. Score 0.519 Round 3: 319 peptides, 44 chains. Longest chain 18 peptides. Score 0.555 Round 4: 306 peptides, 42 chains. Longest chain 19 peptides. Score 0.546 Round 5: 319 peptides, 46 chains. Longest chain 19 peptides. Score 0.536 Taking the results from Round 3 Chains 44, Residues 275, Estimated correctness of the model 13.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8127 restraints for refining 3695 atoms. 7071 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2451 (Rfree = 0.000) for 3695 atoms. Found 17 (24 requested) and removed 18 (13 requested) atoms. Cycle 27: After refmac, R = 0.2422 (Rfree = 0.000) for 3680 atoms. Found 12 (24 requested) and removed 19 (13 requested) atoms. Cycle 28: After refmac, R = 0.2287 (Rfree = 0.000) for 3668 atoms. Found 10 (24 requested) and removed 15 (13 requested) atoms. Cycle 29: After refmac, R = 0.2238 (Rfree = 0.000) for 3655 atoms. Found 5 (24 requested) and removed 14 (13 requested) atoms. Cycle 30: After refmac, R = 0.2205 (Rfree = 0.000) for 3642 atoms. Found 3 (24 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 3755 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3769 seeds are put forward Round 1: 275 peptides, 48 chains. Longest chain 11 peptides. Score 0.409 Round 2: 294 peptides, 42 chains. Longest chain 14 peptides. Score 0.519 Round 3: 317 peptides, 48 chains. Longest chain 12 peptides. Score 0.512 Round 4: 308 peptides, 45 chains. Longest chain 18 peptides. Score 0.521 Round 5: 307 peptides, 45 chains. Longest chain 27 peptides. Score 0.519 Taking the results from Round 4 Chains 45, Residues 263, Estimated correctness of the model 0.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8152 restraints for refining 3695 atoms. 7145 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2378 (Rfree = 0.000) for 3695 atoms. Found 14 (24 requested) and removed 17 (13 requested) atoms. Cycle 32: After refmac, R = 0.2255 (Rfree = 0.000) for 3684 atoms. Found 10 (24 requested) and removed 15 (13 requested) atoms. Cycle 33: After refmac, R = 0.2206 (Rfree = 0.000) for 3675 atoms. Found 6 (24 requested) and removed 13 (13 requested) atoms. Cycle 34: After refmac, R = 0.2140 (Rfree = 0.000) for 3667 atoms. Found 6 (24 requested) and removed 13 (13 requested) atoms. Cycle 35: After refmac, R = 0.2135 (Rfree = 0.000) for 3658 atoms. Found 3 (24 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 3.13 Search for helices and strands: 0 residues in 0 chains, 3746 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 3773 seeds are put forward Round 1: 269 peptides, 49 chains. Longest chain 15 peptides. Score 0.382 Round 2: 296 peptides, 43 chains. Longest chain 16 peptides. Score 0.514 Round 3: 294 peptides, 41 chains. Longest chain 18 peptides. Score 0.529 Round 4: 307 peptides, 46 chains. Longest chain 18 peptides. Score 0.509 Round 5: 305 peptides, 47 chains. Longest chain 18 peptides. Score 0.494 Taking the results from Round 3 Chains 43, Residues 253, Estimated correctness of the model 3.8 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8016 restraints for refining 3695 atoms. 6997 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2332 (Rfree = 0.000) for 3695 atoms. Found 15 (24 requested) and removed 17 (13 requested) atoms. Cycle 37: After refmac, R = 0.2207 (Rfree = 0.000) for 3687 atoms. Found 7 (24 requested) and removed 18 (13 requested) atoms. Cycle 38: After refmac, R = 0.2194 (Rfree = 0.000) for 3672 atoms. Found 7 (24 requested) and removed 14 (13 requested) atoms. Cycle 39: After refmac, R = 0.2154 (Rfree = 0.000) for 3662 atoms. Found 7 (24 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.2205 (Rfree = 0.000) for 3653 atoms. Found 15 (24 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 3773 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3785 seeds are put forward Round 1: 260 peptides, 47 chains. Longest chain 18 peptides. Score 0.381 Round 2: 272 peptides, 43 chains. Longest chain 18 peptides. Score 0.456 Round 3: 271 peptides, 43 chains. Longest chain 16 peptides. Score 0.454 Round 4: 272 peptides, 41 chains. Longest chain 18 peptides. Score 0.478 Round 5: 272 peptides, 42 chains. Longest chain 15 peptides. Score 0.467 Taking the results from Round 4 Chains 41, Residues 231, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8285 restraints for refining 3695 atoms. 7382 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2341 (Rfree = 0.000) for 3695 atoms. Found 11 (24 requested) and removed 19 (13 requested) atoms. Cycle 42: After refmac, R = 0.2187 (Rfree = 0.000) for 3682 atoms. Found 2 (24 requested) and removed 14 (13 requested) atoms. Cycle 43: After refmac, R = 0.2133 (Rfree = 0.000) for 3667 atoms. Found 3 (24 requested) and removed 13 (13 requested) atoms. Cycle 44: After refmac, R = 0.2104 (Rfree = 0.000) for 3652 atoms. Found 6 (24 requested) and removed 14 (13 requested) atoms. Cycle 45: After refmac, R = 0.2107 (Rfree = 0.000) for 3639 atoms. Found 4 (24 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 3743 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3756 seeds are put forward Round 1: 239 peptides, 43 chains. Longest chain 14 peptides. Score 0.370 Round 2: 253 peptides, 41 chains. Longest chain 14 peptides. Score 0.430 Round 3: 259 peptides, 41 chains. Longest chain 18 peptides. Score 0.446 Round 4: 253 peptides, 37 chains. Longest chain 15 peptides. Score 0.475 Round 5: 258 peptides, 42 chains. Longest chain 12 peptides. Score 0.432 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 216, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2it9-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8621 reflections ( 98.45 % complete ) and 8392 restraints for refining 3694 atoms. 7565 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2204 (Rfree = 0.000) for 3694 atoms. Found 0 (24 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2156 (Rfree = 0.000) for 3679 atoms. Found 0 (24 requested) and removed 12 (13 requested) atoms. Cycle 48: After refmac, R = 0.2072 (Rfree = 0.000) for 3666 atoms. Found 0 (24 requested) and removed 5 (13 requested) atoms. Cycle 49: After refmac, R = 0.2091 (Rfree = 0.000) for 3661 atoms. TimeTaking 37.62