null Sun 23 Dec 22:22:52 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 1vpz-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpz-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpz-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-4.0-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/1vpz-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-4.0-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 22:23:02 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/1vpz-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-4.0-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 84 and 0 Target number of residues in the AU: 84 Target solvent content: 0.6678 Checking the provided sequence file Detected sequence length: 73 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 146 Adjusted target solvent content: 0.42 Input MTZ file: 1vpz-4.0-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: 20 Cell parameters: 49.075 56.647 98.468 90.000 90.000 90.000 Input sequence file: 1vpz-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1168 target number of atoms Had to go as low as 0.55 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: 24.580 4.002 Wilson plot Bfac: 90.47 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1242 reflections ( 97.11 % complete ) and 0 restraints for refining 1293 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3751 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2929 (Rfree = 0.000) for 1293 atoms. Found 0 (6 requested) and removed 20 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 4.06 Search for helices and strands: 0 residues in 0 chains, 1280 seeds are put forward NCS extension: 0 residues added, 1280 seeds are put forward Round 1: 23 peptides, 5 chains. Longest chain 6 peptides. Score 0.220 Round 2: 22 peptides, 5 chains. Longest chain 5 peptides. Score 0.203 Round 3: 30 peptides, 7 chains. Longest chain 5 peptides. Score 0.199 Round 4: 27 peptides, 5 chains. Longest chain 7 peptides. Score 0.283 Round 5: 34 peptides, 7 chains. Longest chain 7 peptides. Score 0.259 Taking the results from Round 4 Chains 5, Residues 22, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 3017 restraints for refining 1054 atoms. 2934 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3108 (Rfree = 0.000) for 1054 atoms. Found 3 (5 requested) and removed 17 (2 requested) atoms. Cycle 2: After refmac, R = 0.3111 (Rfree = 0.000) for 1037 atoms. Found 0 (4 requested) and removed 5 (2 requested) atoms. Cycle 3: After refmac, R = 0.2865 (Rfree = 0.000) for 1029 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 4: After refmac, R = 0.2924 (Rfree = 0.000) for 1026 atoms. Found 0 (4 requested) and removed 16 (2 requested) atoms. Cycle 5: After refmac, R = 0.3045 (Rfree = 0.000) for 1010 atoms. Found 0 (4 requested) and removed 17 (2 requested) atoms. WARNING: The data used for computing density maps have negative Wilson B factor WARNING: Is the model/space group correct? ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.73 1.93 Search for helices and strands: 0 residues in 0 chains, 1009 seeds are put forward NCS extension: 0 residues added, 1009 seeds are put forward Round 1: 37 peptides, 8 chains. Longest chain 6 peptides. Score 0.242 Round 2: 42 peptides, 8 chains. Longest chain 7 peptides. Score 0.310 Round 3: 47 peptides, 9 chains. Longest chain 8 peptides. Score 0.320 Round 4: 48 peptides, 8 chains. Longest chain 9 peptides. Score 0.387 Round 5: 45 peptides, 8 chains. Longest chain 8 peptides. Score 0.349 Taking the results from Round 4 Chains 8, Residues 40, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 2483 restraints for refining 951 atoms. 2331 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3053 (Rfree = 0.000) for 951 atoms. Found 2 (4 requested) and removed 14 (2 requested) atoms. Cycle 7: After refmac, R = 0.2769 (Rfree = 0.000) for 923 atoms. Found 3 (4 requested) and removed 8 (2 requested) atoms. Cycle 8: After refmac, R = 0.3739 (Rfree = 0.000) for 915 atoms. Found 4 (4 requested) and removed 14 (2 requested) atoms. Cycle 9: After refmac, R = 0.3827 (Rfree = 0.000) for 889 atoms. Found 3 (4 requested) and removed 4 (2 requested) atoms. Cycle 10: After refmac, R = 0.3914 (Rfree = 0.000) for 878 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. WARNING: The data used for computing density maps have negative Wilson B factor WARNING: Is the model/space group correct? ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.73 1.93 Search for helices and strands: 0 residues in 0 chains, 910 seeds are put forward NCS extension: 0 residues added, 910 seeds are put forward Round 1: 13 peptides, 3 chains. Longest chain 5 peptides. Score 0.190 Round 2: 18 peptides, 3 chains. Longest chain 7 peptides. Score 0.285 Round 3: 22 peptides, 4 chains. Longest chain 8 peptides. Score 0.275 Round 4: 23 peptides, 4 chains. Longest chain 8 peptides. Score 0.291 Round 5: 23 peptides, 4 chains. Longest chain 8 peptides. Score 0.291 Taking the results from Round 5 Chains 4, Residues 19, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 1743 restraints for refining 732 atoms. 1671 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3706 (Rfree = 0.000) for 732 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 12: After refmac, R = 0.3675 (Rfree = 0.000) for 726 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. Cycle 13: After refmac, R = 0.3836 (Rfree = 0.000) for 720 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 14: After refmac, R = 0.4020 (Rfree = 0.000) for 718 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 15: After refmac, R = 0.3932 (Rfree = 0.000) for 714 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. WARNING: The data used for computing density maps have negative Wilson B factor WARNING: Is the model/space group correct? ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.73 1.93 Search for helices and strands: 0 residues in 0 chains, 732 seeds are put forward NCS extension: 0 residues added, 732 seeds are put forward Round 1: 17 peptides, 4 chains. Longest chain 5 peptides. Score 0.187 Round 2: 22 peptides, 5 chains. Longest chain 5 peptides. Score 0.203 Round 3: 25 peptides, 5 chains. Longest chain 7 peptides. Score 0.252 Round 4: 30 peptides, 5 chains. Longest chain 9 peptides. Score 0.326 Round 5: 24 peptides, 5 chains. Longest chain 6 peptides. Score 0.236 Taking the results from Round 4 Chains 5, Residues 25, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 1107 restraints for refining 556 atoms. 1012 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3948 (Rfree = 0.000) for 556 atoms. Found 1 (2 requested) and removed 10 (1 requested) atoms. Cycle 17: After refmac, R = 0.3809 (Rfree = 0.000) for 544 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 18: After refmac, R = 0.4224 (Rfree = 0.000) for 541 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 19: After refmac, R = 0.4006 (Rfree = 0.000) for 541 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 20: After refmac, R = 0.4110 (Rfree = 0.000) for 537 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. WARNING: The data used for computing density maps have negative Wilson B factor WARNING: Is the model/space group correct? ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.73 1.93 Search for helices and strands: 0 residues in 0 chains, 555 seeds are put forward NCS extension: 0 residues added, 555 seeds are put forward Round 1: 19 peptides, 4 chains. Longest chain 5 peptides. Score 0.224 Round 2: 29 peptides, 5 chains. Longest chain 8 peptides. Score 0.312 Round 3: 29 peptides, 5 chains. Longest chain 8 peptides. Score 0.312 Round 4: 30 peptides, 4 chains. Longest chain 10 peptides. Score 0.389 Round 5: 32 peptides, 5 chains. Longest chain 11 peptides. Score 0.354 Taking the results from Round 4 Chains 4, Residues 26, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 847 restraints for refining 467 atoms. 747 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.4279 (Rfree = 0.000) for 467 atoms. Found 2 (2 requested) and removed 11 (1 requested) atoms. Cycle 22: After refmac, R = 0.4308 (Rfree = 0.000) for 457 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 23: After refmac, R = 0.4161 (Rfree = 0.000) for 456 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 24: After refmac, R = 0.4534 (Rfree = 0.000) for 454 atoms. Found 2 (2 requested) and removed 24 (1 requested) atoms. Cycle 25: After refmac, R = 0.4321 (Rfree = 0.000) for 432 atoms. Found 2 (2 requested) and removed 16 (1 requested) atoms. WARNING: The data used for computing density maps have negative Wilson B factor WARNING: Is the model/space group correct? ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.73 1.93 Search for helices and strands: 0 residues in 0 chains, 439 seeds are put forward NCS extension: 0 residues added, 439 seeds are put forward Round 1: 8 peptides, 2 chains. Longest chain 4 peptides. Score 0.167 Round 2: 15 peptides, 3 chains. Longest chain 6 peptides. Score 0.231 Round 3: 18 peptides, 4 chains. Longest chain 6 peptides. Score 0.206 Round 4: 15 peptides, 3 chains. Longest chain 5 peptides. Score 0.231 Round 5: 20 peptides, 3 chains. Longest chain 8 peptides. Score 0.317 Taking the results from Round 5 Chains 3, Residues 17, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 727 restraints for refining 390 atoms. 662 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 26: After refmac, R = 0.4791 (Rfree = 0.000) for 390 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. Cycle 27: After refmac, R = 0.4489 (Rfree = 0.000) for 385 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 28: After refmac, R = 0.4652 (Rfree = 0.000) for 382 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. Cycle 29: After refmac, R = 0.4309 (Rfree = 0.000) for 378 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 30: After refmac, R = 0.4329 (Rfree = 0.000) for 378 atoms. Found 2 (2 requested) and removed 4 (1 requested) atoms. WARNING: The data used for computing density maps have negative Wilson B factor WARNING: Is the model/space group correct? ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.73 1.93 Search for helices and strands: 0 residues in 0 chains, 392 seeds are put forward NCS extension: 0 residues added, 392 seeds are put forward Round 1: 42 peptides, 8 chains. Longest chain 8 peptides. Score 0.310 Round 2: 44 peptides, 8 chains. Longest chain 9 peptides. Score 0.337 Round 3: 43 peptides, 8 chains. Longest chain 8 peptides. Score 0.324 Round 4: 41 peptides, 7 chains. Longest chain 8 peptides. Score 0.354 Round 5: 44 peptides, 7 chains. Longest chain 9 peptides. Score 0.392 Taking the results from Round 5 Chains 7, Residues 37, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 852 restraints for refining 468 atoms. 711 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.4369 (Rfree = 0.000) for 468 atoms. Found 2 (2 requested) and removed 13 (1 requested) atoms. Cycle 32: After refmac, R = 0.4301 (Rfree = 0.000) for 454 atoms. Found 1 (2 requested) and removed 4 (1 requested) atoms. Cycle 33: After refmac, R = 0.4164 (Rfree = 0.000) for 449 atoms. Found 2 (2 requested) and removed 7 (1 requested) atoms. Cycle 34: After refmac, R = 0.4327 (Rfree = 0.000) for 441 atoms. Found 2 (2 requested) and removed 6 (1 requested) atoms. Cycle 35: After refmac, R = 0.4515 (Rfree = 0.000) for 436 atoms. Found 2 (2 requested) and removed 7 (1 requested) atoms. WARNING: The data used for computing density maps have negative Wilson B factor WARNING: Is the model/space group correct? ------------------------------------------------------ Building Cycle 8 Atomic shape factors 0.00 0.00 Search for helices and strands: 0 residues in 0 chains, 446 seeds are put forward NCS extension: 0 residues added, 446 seeds are put forward Round 1: 33 peptides, 7 chains. Longest chain 5 peptides. Score 0.244 Round 2: 41 peptides, 8 chains. Longest chain 7 peptides. Score 0.297 Round 3: 36 peptides, 7 chains. Longest chain 7 peptides. Score 0.287 Round 4: 33 peptides, 6 chains. Longest chain 7 peptides. Score 0.306 Round 5: 33 peptides, 5 chains. Longest chain 9 peptides. Score 0.367 Taking the results from Round 5 Chains 5, Residues 28, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 1096 restraints for refining 516 atoms. 989 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.4384 (Rfree = 0.000) for 516 atoms. Found 2 (2 requested) and removed 14 (1 requested) atoms. Cycle 37: After refmac, R = 0.4762 (Rfree = 0.000) for 503 atoms. Found 2 (2 requested) and removed 12 (1 requested) atoms. Cycle 38: After refmac, R = 0.4501 (Rfree = 0.000) for 493 atoms. Found 2 (2 requested) and removed 4 (1 requested) atoms. Cycle 39: After refmac, R = 0.4695 (Rfree = 0.000) for 491 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. Cycle 40: After refmac, R = 0.4259 (Rfree = 0.000) for 488 atoms. Found 1 (2 requested) and removed 4 (1 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.95 3.28 Search for helices and strands: 0 residues in 0 chains, 496 seeds are put forward NCS extension: 0 residues added, 496 seeds are put forward Round 1: 36 peptides, 7 chains. Longest chain 10 peptides. Score 0.287 Round 2: 38 peptides, 7 chains. Longest chain 8 peptides. Score 0.315 Round 3: 37 peptides, 7 chains. Longest chain 9 peptides. Score 0.301 Round 4: 35 peptides, 6 chains. Longest chain 12 peptides. Score 0.333 Round 5: 33 peptides, 7 chains. Longest chain 8 peptides. Score 0.244 Taking the results from Round 4 Chains 6, Residues 29, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1242 reflections ( 97.11 % complete ) and 1068 restraints for refining 540 atoms. 958 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.4433 (Rfree = 0.000) for 540 atoms. Found 2 (2 requested) and removed 7 (1 requested) atoms. Cycle 42: After refmac, R = 0.4231 (Rfree = 0.000) for 532 atoms. Found 2 (2 requested) and removed 6 (1 requested) atoms. Cycle 43: After refmac, R = 0.4108 (Rfree = 0.000) for 528 atoms. Found 2 (2 requested) and removed 6 (1 requested) atoms. Cycle 44: After refmac, R = 0.4027 (Rfree = 0.000) for 524 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 45: After refmac, R = 0.4131 (Rfree = 0.000) for 523 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.99 3.33 Search for helices and strands: 0 residues in 0 chains, 529 seeds are put forward NCS extension: 0 residues added, 529 seeds are put forward Round 1: 27 peptides, 6 chains. Longest chain 6 peptides. Score 0.217 Round 2: 33 peptides, 5 chains. Longest chain 10 peptides. Score 0.367 Round 3: 41 peptides, 7 chains. Longest chain 11 peptides. Score 0.354 Round 4: 37 peptides, 6 chains. Longest chain 9 peptides. Score 0.360 Round 5: 44 peptides, 8 chains. Longest chain 12 peptides. Score 0.337 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 5, 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 1vpz-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1242 reflections ( 97.11 % complete ) and 1010 restraints for refining 511 atoms. 903 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.4403 (Rfree = 0.000) for 511 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Cycle 47: After refmac, R = 0.4271 (Rfree = 0.000) for 510 atoms. Found 0 (2 requested) and removed 0 (1 requested) atoms. Cycle 48: After refmac, R = 0.4253 (Rfree = 0.000) for 510 atoms. Found 0 (2 requested) and removed 0 (1 requested) atoms. Cycle 49: After refmac, R = 0.4248 (Rfree = 0.000) for 510 atoms. Found 0 (2 requested) and removed 0 (1 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:42:54 GMT 2018 Job finished. TimeTaking 20.03 Used memory is bytes: 11873648