Sun 23 Dec 22:23:05 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 1vmg-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmg-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmg-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-3.2-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/1vmg-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-3.2-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 22:23:15 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/1vmg-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-3.2-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 106 and 0 Target number of residues in the AU: 106 Target solvent content: 0.6238 Checking the provided sequence file Detected sequence length: 95 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 95 Adjusted target solvent content: 0.66 Input MTZ file: 1vmg-3.2-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: 98 Cell parameters: 79.748 79.748 95.906 90.000 90.000 90.000 Input sequence file: 1vmg-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 760 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 Loops will be built when appropriate and at the last cycle Resolution range: 61.319 3.200 Wilson plot Bfac: 61.94 2739 reflections ( 99.71 % complete ) and 0 restraints for refining 841 atoms. Observations/parameters ratio is 0.81 ------------------------------------------------------ Starting model: R = 0.3327 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3678 (Rfree = 0.000) for 841 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 2.55 Search for helices and strands: 0 residues in 0 chains, 864 seeds are put forward Round 1: 54 peptides, 10 chains. Longest chain 10 peptides. Score 0.340 Round 2: 55 peptides, 6 chains. Longest chain 18 peptides. Score 0.534 Round 3: 50 peptides, 7 chains. Longest chain 11 peptides. Score 0.440 Round 4: 48 peptides, 6 chains. Longest chain 13 peptides. Score 0.467 Round 5: 51 peptides, 6 chains. Longest chain 13 peptides. Score 0.497 Taking the results from Round 2 Chains 6, Residues 49, Estimated correctness of the model 22.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2739 reflections ( 99.71 % complete ) and 1441 restraints for refining 693 atoms. 1251 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3899 (Rfree = 0.000) for 693 atoms. Found 6 (6 requested) and removed 25 (3 requested) atoms. Cycle 2: After refmac, R = 0.3942 (Rfree = 0.000) for 660 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 3: After refmac, R = 0.3788 (Rfree = 0.000) for 644 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 4: After refmac, R = 0.3749 (Rfree = 0.000) for 635 atoms. Found 5 (5 requested) and removed 13 (2 requested) atoms. Cycle 5: After refmac, R = 0.3682 (Rfree = 0.000) for 619 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.09 2.48 Search for helices and strands: 0 residues in 0 chains, 669 seeds are put forward Round 1: 50 peptides, 8 chains. Longest chain 13 peptides. Score 0.392 Round 2: 55 peptides, 8 chains. Longest chain 11 peptides. Score 0.445 Round 3: 55 peptides, 7 chains. Longest chain 10 peptides. Score 0.490 Round 4: 60 peptides, 6 chains. Longest chain 14 peptides. Score 0.578 Round 5: 60 peptides, 6 chains. Longest chain 15 peptides. Score 0.578 Taking the results from Round 5 Chains 6, Residues 54, Estimated correctness of the model 35.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2739 reflections ( 99.71 % complete ) and 1323 restraints for refining 647 atoms. 1113 conditional restraints added. Observations/parameters ratio is 1.06 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3477 (Rfree = 0.000) for 647 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 7: After refmac, R = 0.3223 (Rfree = 0.000) for 646 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 8: After refmac, R = 0.3288 (Rfree = 0.000) for 643 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 9: After refmac, R = 0.3187 (Rfree = 0.000) for 644 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 10: After refmac, R = 0.3391 (Rfree = 0.000) for 647 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.61 2.09 Search for helices and strands: 0 residues in 0 chains, 693 seeds are put forward Round 1: 70 peptides, 9 chains. Longest chain 16 peptides. Score 0.544 Round 2: 67 peptides, 8 chains. Longest chain 14 peptides. Score 0.558 Round 3: 61 peptides, 7 chains. Longest chain 15 peptides. Score 0.546 Round 4: 65 peptides, 6 chains. Longest chain 24 peptides. Score 0.619 Round 5: 64 peptides, 7 chains. Longest chain 17 peptides. Score 0.572 Taking the results from Round 4 Chains 6, Residues 59, Estimated correctness of the model 46.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2739 reflections ( 99.71 % complete ) and 1404 restraints for refining 683 atoms. 1174 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3311 (Rfree = 0.000) for 683 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 12: After refmac, R = 0.3193 (Rfree = 0.000) for 672 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 13: After refmac, R = 0.2988 (Rfree = 0.000) for 670 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 14: After refmac, R = 0.2982 (Rfree = 0.000) for 670 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 15: After refmac, R = 0.3014 (Rfree = 0.000) for 669 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.09 2.48 Search for helices and strands: 0 residues in 0 chains, 697 seeds are put forward Round 1: 53 peptides, 7 chains. Longest chain 10 peptides. Score 0.471 Round 2: 61 peptides, 7 chains. Longest chain 12 peptides. Score 0.546 Round 3: 61 peptides, 7 chains. Longest chain 11 peptides. Score 0.546 Round 4: 58 peptides, 7 chains. Longest chain 12 peptides. Score 0.519 Round 5: 62 peptides, 7 chains. Longest chain 12 peptides. Score 0.555 Taking the results from Round 5 Chains 7, Residues 55, Estimated correctness of the model 28.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2739 reflections ( 99.71 % complete ) and 1393 restraints for refining 664 atoms. 1180 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3313 (Rfree = 0.000) for 664 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 17: After refmac, R = 0.3229 (Rfree = 0.000) for 661 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 18: After refmac, R = 0.3002 (Rfree = 0.000) for 660 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 19: After refmac, R = 0.2876 (Rfree = 0.000) for 660 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 20: After refmac, R = 0.3200 (Rfree = 0.000) for 662 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.90 2.33 Search for helices and strands: 0 residues in 0 chains, 704 seeds are put forward Round 1: 68 peptides, 7 chains. Longest chain 27 peptides. Score 0.605 Round 2: 65 peptides, 5 chains. Longest chain 27 peptides. Score 0.656 Round 3: 70 peptides, 4 chains. Longest chain 38 peptides. Score 0.723 Round 4: 68 peptides, 4 chains. Longest chain 39 peptides. Score 0.710 Round 5: 60 peptides, 6 chains. Longest chain 17 peptides. Score 0.578 Taking the results from Round 3 Chains 4, Residues 66, Estimated correctness of the model 69.9 % 1 chains (37 residues) have been docked in sequence ------------------------------------------------------ 2739 reflections ( 99.71 % complete ) and 1026 restraints for refining 701 atoms. 589 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3233 (Rfree = 0.000) for 701 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.3133 (Rfree = 0.000) for 697 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 23: After refmac, R = 0.2937 (Rfree = 0.000) for 694 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 24: After refmac, R = 0.2484 (Rfree = 0.000) for 689 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 25: After refmac, R = 0.2275 (Rfree = 0.000) for 688 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 2.57 Search for helices and strands: 0 residues in 0 chains, 717 seeds are put forward Round 1: 59 peptides, 7 chains. Longest chain 16 peptides. Score 0.528 Round 2: 67 peptides, 5 chains. Longest chain 25 peptides. Score 0.670 Round 3: 62 peptides, 7 chains. Longest chain 15 peptides. Score 0.555 Round 4: 63 peptides, 7 chains. Longest chain 15 peptides. Score 0.564 Round 5: 58 peptides, 8 chains. Longest chain 15 peptides. Score 0.475 Taking the results from Round 2 Chains 5, Residues 62, Estimated correctness of the model 58.5 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 2739 reflections ( 99.71 % complete ) and 1191 restraints for refining 693 atoms. 819 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3491 (Rfree = 0.000) for 693 atoms. Found 5 (5 requested) and removed 49 (3 requested) atoms. Cycle 27: After refmac, R = 0.3152 (Rfree = 0.000) for 644 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 28: After refmac, R = 0.2846 (Rfree = 0.000) for 641 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 29: After refmac, R = 0.3290 (Rfree = 0.000) for 635 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 30: After refmac, R = 0.2743 (Rfree = 0.000) for 633 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 2.52 Search for helices and strands: 0 residues in 0 chains, 667 seeds are put forward Round 1: 62 peptides, 8 chains. Longest chain 14 peptides. Score 0.513 Round 2: 71 peptides, 6 chains. Longest chain 32 peptides. Score 0.663 Round 3: 70 peptides, 6 chains. Longest chain 33 peptides. Score 0.656 Round 4: 70 peptides, 6 chains. Longest chain 32 peptides. Score 0.656 Round 5: 64 peptides, 7 chains. Longest chain 17 peptides. Score 0.572 Taking the results from Round 2 Chains 6, Residues 65, Estimated correctness of the model 56.9 % 1 chains (31 residues) have been docked in sequence ------------------------------------------------------ 2739 reflections ( 99.71 % complete ) and 1082 restraints for refining 693 atoms. 673 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3429 (Rfree = 0.000) for 693 atoms. Found 5 (5 requested) and removed 10 (3 requested) atoms. Cycle 32: After refmac, R = 0.3003 (Rfree = 0.000) for 682 atoms. Found 5 (5 requested) and removed 4 (3 requested) atoms. Cycle 33: After refmac, R = 0.2847 (Rfree = 0.000) for 681 atoms. Found 5 (5 requested) and removed 7 (3 requested) atoms. Cycle 34: After refmac, R = 0.2949 (Rfree = 0.000) for 678 atoms. Found 5 (5 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.3041 (Rfree = 0.000) for 678 atoms. Found 5 (5 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.04 2.44 Search for helices and strands: 0 residues in 0 chains, 712 seeds are put forward Round 1: 63 peptides, 6 chains. Longest chain 22 peptides. Score 0.603 Round 2: 70 peptides, 6 chains. Longest chain 34 peptides. Score 0.656 Round 3: 64 peptides, 5 chains. Longest chain 37 peptides. Score 0.649 Round 4: 67 peptides, 8 chains. Longest chain 14 peptides. Score 0.558 Round 5: 63 peptides, 8 chains. Longest chain 25 peptides. Score 0.523 Taking the results from Round 2 Chains 6, Residues 64, Estimated correctness of the model 55.3 % 1 chains (33 residues) have been docked in sequence ------------------------------------------------------ 2739 reflections ( 99.71 % complete ) and 1034 restraints for refining 693 atoms. 619 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3406 (Rfree = 0.000) for 693 atoms. Found 5 (5 requested) and removed 5 (3 requested) atoms. Cycle 37: After refmac, R = 0.3062 (Rfree = 0.000) for 687 atoms. Found 5 (5 requested) and removed 4 (3 requested) atoms. Cycle 38: After refmac, R = 0.3310 (Rfree = 0.000) for 682 atoms. Found 5 (5 requested) and removed 3 (3 requested) atoms. Cycle 39: After refmac, R = 0.2952 (Rfree = 0.000) for 683 atoms. Found 4 (5 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.2862 (Rfree = 0.000) for 679 atoms. Found 4 (5 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 2.52 Search for helices and strands: 0 residues in 0 chains, 707 seeds are put forward Round 1: 63 peptides, 7 chains. Longest chain 21 peptides. Score 0.564 Round 2: 66 peptides, 8 chains. Longest chain 23 peptides. Score 0.549 Round 3: 64 peptides, 7 chains. Longest chain 26 peptides. Score 0.572 Round 4: 65 peptides, 10 chains. Longest chain 13 peptides. Score 0.456 Round 5: 67 peptides, 8 chains. Longest chain 20 peptides. Score 0.558 Taking the results from Round 3 Chains 7, Residues 57, Estimated correctness of the model 33.3 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 2739 reflections ( 99.71 % complete ) and 1122 restraints for refining 693 atoms. 772 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3335 (Rfree = 0.000) for 693 atoms. Found 5 (5 requested) and removed 7 (3 requested) atoms. Cycle 42: After refmac, R = 0.3384 (Rfree = 0.000) for 685 atoms. Found 5 (5 requested) and removed 11 (3 requested) atoms. Cycle 43: After refmac, R = 0.3366 (Rfree = 0.000) for 673 atoms. Found 5 (5 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.3291 (Rfree = 0.000) for 669 atoms. Found 5 (5 requested) and removed 4 (3 requested) atoms. Cycle 45: After refmac, R = 0.3255 (Rfree = 0.000) for 661 atoms. Found 5 (5 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.04 2.44 Search for helices and strands: 0 residues in 0 chains, 723 seeds are put forward Round 1: 63 peptides, 8 chains. Longest chain 19 peptides. Score 0.523 Round 2: 59 peptides, 9 chains. Longest chain 16 peptides. Score 0.440 Round 3: 65 peptides, 7 chains. Longest chain 24 peptides. Score 0.581 Round 4: 68 peptides, 6 chains. Longest chain 32 peptides. Score 0.642 Round 5: 59 peptides, 6 chains. Longest chain 23 peptides. Score 0.570 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 62, Estimated correctness of the model 51.9 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vmg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2739 reflections ( 99.71 % complete ) and 1397 restraints for refining 693 atoms. 1155 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3403 (Rfree = 0.000) for 693 atoms. Found 0 (5 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3116 (Rfree = 0.000) for 688 atoms. Found 0 (5 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3593 (Rfree = 0.000) for 682 atoms. Found 0 (5 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3151 (Rfree = 0.000) for 679 atoms. TimeTaking 23.98