Sun 23 Dec 22:22:59 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 2ilb-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ilb-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ilb-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-3.4-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/2ilb-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-3.4-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 22:23:08 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/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-3.4-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 71 and 0 Target number of residues in the AU: 71 Target solvent content: 0.6435 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 114 Adjusted target solvent content: 0.43 Input MTZ file: 2ilb-3.4-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: 5 Cell parameters: 48.900 72.000 32.740 90.000 110.754 90.000 Input sequence file: 2ilb-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 912 target number of atoms Had to go as low as 0.70 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 Loops will be built when appropriate and at the last cycle Resolution range: 38.600 3.401 Wilson plot Bfac: 72.75 1490 reflections ( 99.47 % complete ) and 0 restraints for refining 1016 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3365 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2859 (Rfree = 0.000) for 1016 atoms. Found 2 (7 requested) and removed 27 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.66 Search for helices and strands: 0 residues in 0 chains, 998 seeds are put forward Round 1: 29 peptides, 7 chains. Longest chain 5 peptides. Score 0.186 Round 2: 41 peptides, 9 chains. Longest chain 7 peptides. Score 0.253 Round 3: 46 peptides, 8 chains. Longest chain 10 peptides. Score 0.399 Round 4: 57 peptides, 11 chains. Longest chain 13 peptides. Score 0.374 Round 5: 45 peptides, 8 chains. Longest chain 11 peptides. Score 0.384 Taking the results from Round 3 Chains 8, Residues 38, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 1490 reflections ( 99.47 % complete ) and 1811 restraints for refining 829 atoms. 1641 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3370 (Rfree = 0.000) for 829 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Cycle 2: After refmac, R = 0.3144 (Rfree = 0.000) for 810 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 3: After refmac, R = 0.3476 (Rfree = 0.000) for 792 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 4: After refmac, R = 0.3576 (Rfree = 0.000) for 782 atoms. Found 4 (5 requested) and removed 21 (2 requested) atoms. Cycle 5: After refmac, R = 0.3346 (Rfree = 0.000) for 756 atoms. Found 3 (5 requested) and removed 31 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 4.21 Search for helices and strands: 0 residues in 0 chains, 760 seeds are put forward Round 1: 27 peptides, 6 chains. Longest chain 6 peptides. Score 0.225 Round 2: 39 peptides, 8 chains. Longest chain 7 peptides. Score 0.289 Round 3: 34 peptides, 7 chains. Longest chain 6 peptides. Score 0.276 Round 4: 38 peptides, 6 chains. Longest chain 13 peptides. Score 0.410 Round 5: 34 peptides, 6 chains. Longest chain 11 peptides. Score 0.347 Taking the results from Round 4 Chains 6, Residues 32, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 1490 reflections ( 99.47 % complete ) and 1403 restraints for refining 678 atoms. 1271 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3294 (Rfree = 0.000) for 678 atoms. Found 4 (5 requested) and removed 7 (2 requested) atoms. Cycle 7: After refmac, R = 0.3055 (Rfree = 0.000) for 669 atoms. Found 5 (5 requested) and removed 17 (2 requested) atoms. Cycle 8: After refmac, R = 0.3167 (Rfree = 0.000) for 653 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 9: After refmac, R = 0.3236 (Rfree = 0.000) for 648 atoms. Found 4 (4 requested) and removed 21 (2 requested) atoms. Cycle 10: After refmac, R = 0.3501 (Rfree = 0.000) for 627 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.95 4.34 Search for helices and strands: 0 residues in 0 chains, 649 seeds are put forward Round 1: 32 peptides, 7 chains. Longest chain 6 peptides. Score 0.241 Round 2: 48 peptides, 10 chains. Longest chain 7 peptides. Score 0.300 Round 3: 39 peptides, 7 chains. Longest chain 10 peptides. Score 0.358 Round 4: 42 peptides, 8 chains. Longest chain 8 peptides. Score 0.338 Round 5: 46 peptides, 8 chains. Longest chain 9 peptides. Score 0.399 Taking the results from Round 5 Chains 8, Residues 38, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 1490 reflections ( 99.47 % complete ) and 1345 restraints for refining 679 atoms. 1187 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3276 (Rfree = 0.000) for 679 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 12: After refmac, R = 0.3101 (Rfree = 0.000) for 661 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 13: After refmac, R = 0.2968 (Rfree = 0.000) for 653 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 14: After refmac, R = 0.3284 (Rfree = 0.000) for 646 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 15: After refmac, R = 0.2920 (Rfree = 0.000) for 635 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.80 4.17 Search for helices and strands: 0 residues in 0 chains, 662 seeds are put forward Round 1: 43 peptides, 10 chains. Longest chain 7 peptides. Score 0.218 Round 2: 47 peptides, 9 chains. Longest chain 7 peptides. Score 0.350 Round 3: 58 peptides, 11 chains. Longest chain 8 peptides. Score 0.389 Round 4: 53 peptides, 9 chains. Longest chain 10 peptides. Score 0.438 Round 5: 52 peptides, 7 chains. Longest chain 13 peptides. Score 0.541 Taking the results from Round 5 Chains 8, Residues 45, Estimated correctness of the model 8.2 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1490 reflections ( 99.47 % complete ) and 1427 restraints for refining 707 atoms. 1227 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3494 (Rfree = 0.000) for 707 atoms. Found 5 (5 requested) and removed 15 (2 requested) atoms. Cycle 17: After refmac, R = 0.3444 (Rfree = 0.000) for 688 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 18: After refmac, R = 0.3597 (Rfree = 0.000) for 674 atoms. Found 5 (5 requested) and removed 14 (2 requested) atoms. Cycle 19: After refmac, R = 0.3248 (Rfree = 0.000) for 658 atoms. Found 5 (5 requested) and removed 27 (2 requested) atoms. Cycle 20: After refmac, R = 0.3375 (Rfree = 0.000) for 634 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.98 4.37 Search for helices and strands: 0 residues in 0 chains, 652 seeds are put forward Round 1: 36 peptides, 8 chains. Longest chain 7 peptides. Score 0.238 Round 2: 38 peptides, 7 chains. Longest chain 7 peptides. Score 0.342 Round 3: 35 peptides, 5 chains. Longest chain 11 peptides. Score 0.432 Round 4: 42 peptides, 7 chains. Longest chain 8 peptides. Score 0.404 Round 5: 41 peptides, 7 chains. Longest chain 8 peptides. Score 0.389 Taking the results from Round 3 Chains 5, Residues 30, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1490 reflections ( 99.47 % complete ) and 1450 restraints for refining 642 atoms. 1335 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3660 (Rfree = 0.000) for 642 atoms. Found 4 (4 requested) and removed 14 (2 requested) atoms. Cycle 22: After refmac, R = 0.3625 (Rfree = 0.000) for 626 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 23: After refmac, R = 0.3332 (Rfree = 0.000) for 614 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 24: After refmac, R = 0.3482 (Rfree = 0.000) for 609 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 25: After refmac, R = 0.3251 (Rfree = 0.000) for 604 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 4.22 Search for helices and strands: 0 residues in 0 chains, 624 seeds are put forward Round 1: 25 peptides, 6 chains. Longest chain 5 peptides. Score 0.187 Round 2: 28 peptides, 5 chains. Longest chain 9 peptides. Score 0.320 Round 3: 25 peptides, 4 chains. Longest chain 8 peptides. Score 0.345 Round 4: 29 peptides, 4 chains. Longest chain 10 peptides. Score 0.411 Round 5: 30 peptides, 4 chains. Longest chain 11 peptides. Score 0.426 Taking the results from Round 5 Chains 4, Residues 26, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1490 reflections ( 99.47 % complete ) and 1352 restraints for refining 615 atoms. 1252 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3463 (Rfree = 0.000) for 615 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 27: After refmac, R = 0.3312 (Rfree = 0.000) for 607 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 28: After refmac, R = 0.3328 (Rfree = 0.000) for 603 atoms. Found 4 (4 requested) and removed 182 (2 requested) atoms. Cycle 29: After refmac, R = 0.3568 (Rfree = 0.000) for 423 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. Cycle 30: After refmac, R = 0.3575 (Rfree = 0.000) for 419 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 4.09 Search for helices and strands: 0 residues in 0 chains, 450 seeds are put forward Round 1: 17 peptides, 4 chains. Longest chain 5 peptides. Score 0.190 Round 2: 27 peptides, 5 chains. Longest chain 7 peptides. Score 0.303 Round 3: 30 peptides, 5 chains. Longest chain 8 peptides. Score 0.354 Round 4: 33 peptides, 6 chains. Longest chain 8 peptides. Score 0.331 Round 5: 35 peptides, 5 chains. Longest chain 9 peptides. Score 0.432 Taking the results from Round 5 Chains 5, Residues 30, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1490 reflections ( 99.47 % complete ) and 935 restraints for refining 487 atoms. 820 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3567 (Rfree = 0.000) for 487 atoms. Found 3 (3 requested) and removed 6 (1 requested) atoms. Cycle 32: After refmac, R = 0.3719 (Rfree = 0.000) for 483 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 33: After refmac, R = 0.3642 (Rfree = 0.000) for 480 atoms. Found 3 (3 requested) and removed 10 (1 requested) atoms. Cycle 34: After refmac, R = 0.3302 (Rfree = 0.000) for 468 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 35: After refmac, R = 0.3320 (Rfree = 0.000) for 468 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.89 Search for helices and strands: 0 residues in 0 chains, 493 seeds are put forward Round 1: 31 peptides, 6 chains. Longest chain 7 peptides. Score 0.297 Round 2: 38 peptides, 6 chains. Longest chain 12 peptides. Score 0.410 Round 3: 39 peptides, 6 chains. Longest chain 10 peptides. Score 0.425 Round 4: 39 peptides, 7 chains. Longest chain 10 peptides. Score 0.358 Round 5: 45 peptides, 8 chains. Longest chain 8 peptides. Score 0.384 Taking the results from Round 3 Chains 6, Residues 33, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 1490 reflections ( 99.47 % complete ) and 1034 restraints for refining 537 atoms. 897 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3754 (Rfree = 0.000) for 537 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 37: After refmac, R = 0.3515 (Rfree = 0.000) for 528 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 38: After refmac, R = 0.3413 (Rfree = 0.000) for 519 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. Cycle 39: After refmac, R = 0.3067 (Rfree = 0.000) for 513 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 40: After refmac, R = 0.3015 (Rfree = 0.000) for 509 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.90 Search for helices and strands: 0 residues in 0 chains, 544 seeds are put forward Round 1: 33 peptides, 7 chains. Longest chain 7 peptides. Score 0.258 Round 2: 37 peptides, 6 chains. Longest chain 9 peptides. Score 0.395 Round 3: 45 peptides, 7 chains. Longest chain 13 peptides. Score 0.448 Round 4: 51 peptides, 8 chains. Longest chain 15 peptides. Score 0.471 Round 5: 50 peptides, 7 chains. Longest chain 12 peptides. Score 0.516 Taking the results from Round 5 Chains 7, Residues 43, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 1490 reflections ( 99.47 % complete ) and 1190 restraints for refining 626 atoms. 996 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3242 (Rfree = 0.000) for 626 atoms. Found 4 (4 requested) and removed 98 (2 requested) atoms. Cycle 42: After refmac, R = 0.3541 (Rfree = 0.000) for 524 atoms. Found 4 (4 requested) and removed 27 (2 requested) atoms. Cycle 43: After refmac, R = 0.3598 (Rfree = 0.000) for 493 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 44: After refmac, R = 0.3072 (Rfree = 0.000) for 486 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 45: After refmac, R = 0.3292 (Rfree = 0.000) for 482 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 4.01 Search for helices and strands: 0 residues in 0 chains, 535 seeds are put forward Round 1: 29 peptides, 6 chains. Longest chain 8 peptides. Score 0.262 Round 2: 27 peptides, 5 chains. Longest chain 9 peptides. Score 0.303 Round 3: 34 peptides, 6 chains. Longest chain 9 peptides. Score 0.347 Round 4: 32 peptides, 7 chains. Longest chain 7 peptides. Score 0.241 Round 5: 32 peptides, 6 chains. Longest chain 8 peptides. Score 0.314 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 28, 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 2ilb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1490 reflections ( 99.47 % complete ) and 1024 restraints for refining 521 atoms. 918 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3296 (Rfree = 0.000) for 521 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 47: After refmac, R = 0.3658 (Rfree = 0.000) for 518 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 48: After refmac, R = 0.3281 (Rfree = 0.000) for 514 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 49: After refmac, R = 0.3180 (Rfree = 0.000) for 512 atoms. TimeTaking 19.98