Mon 24 Dec 07:28:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2itb-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2itb-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2itb-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2itb-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2itb-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2itb-4.0-parrot-noncs ############### 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 07:28:59 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/noncs/ArpWArp/wArpResults/WorkingDir/2itb-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2itb-4.0-parrot-noncs/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 221 and 0 Target number of residues in the AU: 221 Target solvent content: 0.6695 Checking the provided sequence file Detected sequence length: 206 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 412 Adjusted target solvent content: 0.38 Input MTZ file: 2itb-4.0-parrot-noncs.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: 61.232 70.168 84.235 90.000 90.000 90.000 Input sequence file: 2itb-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 3296 target number of atoms Had to go as low as 0.60 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: 53.913 4.000 Wilson plot Bfac: 92.15 3315 reflections ( 99.55 % complete ) and 0 restraints for refining 3627 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3684 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3362 (Rfree = 0.000) for 3627 atoms. Found 7 (17 requested) and removed 27 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.05 4.77 Search for helices and strands: 0 residues in 0 chains, 3711 seeds are put forward NCS extension: 0 residues added, 3711 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 9 peptides. Score 0.261 Round 2: 112 peptides, 19 chains. Longest chain 12 peptides. Score 0.361 Round 3: 125 peptides, 21 chains. Longest chain 16 peptides. Score 0.380 Round 4: 132 peptides, 21 chains. Longest chain 11 peptides. Score 0.412 Round 5: 147 peptides, 23 chains. Longest chain 21 peptides. Score 0.439 Taking the results from Round 5 Chains 23, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 7169 restraints for refining 2914 atoms. 6696 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2821 (Rfree = 0.000) for 2914 atoms. Found 5 (13 requested) and removed 15 (6 requested) atoms. Cycle 2: After refmac, R = 0.2719 (Rfree = 0.000) for 2862 atoms. Found 3 (13 requested) and removed 11 (6 requested) atoms. Cycle 3: After refmac, R = 0.2674 (Rfree = 0.000) for 2841 atoms. Found 2 (13 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.2664 (Rfree = 0.000) for 2831 atoms. Found 2 (13 requested) and removed 8 (6 requested) atoms. Cycle 5: After refmac, R = 0.2667 (Rfree = 0.000) for 2823 atoms. Found 4 (13 requested) and removed 18 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.01 4.72 Search for helices and strands: 0 residues in 0 chains, 2923 seeds are put forward NCS extension: 41 residues added (1 deleted due to clashes), 2964 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 7 peptides. Score 0.240 Round 2: 118 peptides, 22 chains. Longest chain 10 peptides. Score 0.327 Round 3: 122 peptides, 20 chains. Longest chain 12 peptides. Score 0.387 Round 4: 127 peptides, 20 chains. Longest chain 16 peptides. Score 0.410 Round 5: 128 peptides, 19 chains. Longest chain 16 peptides. Score 0.434 Taking the results from Round 5 Chains 19, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 6726 restraints for refining 2699 atoms. 6309 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2928 (Rfree = 0.000) for 2699 atoms. Found 8 (12 requested) and removed 11 (6 requested) atoms. Cycle 7: After refmac, R = 0.2792 (Rfree = 0.000) for 2684 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. Cycle 8: After refmac, R = 0.2736 (Rfree = 0.000) for 2673 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 9: After refmac, R = 0.2730 (Rfree = 0.000) for 2665 atoms. Found 0 (12 requested) and removed 9 (6 requested) atoms. Cycle 10: After refmac, R = 0.2716 (Rfree = 0.000) for 2655 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.97 4.67 Search for helices and strands: 0 residues in 0 chains, 2771 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2783 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 8 peptides. Score 0.250 Round 2: 127 peptides, 22 chains. Longest chain 12 peptides. Score 0.369 Round 3: 119 peptides, 21 chains. Longest chain 10 peptides. Score 0.352 Round 4: 127 peptides, 21 chains. Longest chain 12 peptides. Score 0.390 Round 5: 123 peptides, 21 chains. Longest chain 12 peptides. Score 0.371 Taking the results from Round 4 Chains 21, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 6470 restraints for refining 2618 atoms. 6067 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2923 (Rfree = 0.000) for 2618 atoms. Found 4 (12 requested) and removed 10 (6 requested) atoms. Cycle 12: After refmac, R = 0.2802 (Rfree = 0.000) for 2605 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 13: After refmac, R = 0.2739 (Rfree = 0.000) for 2595 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.2717 (Rfree = 0.000) for 2586 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.2659 (Rfree = 0.000) for 2578 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.95 4.65 Search for helices and strands: 0 residues in 0 chains, 2685 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2700 seeds are put forward Round 1: 129 peptides, 28 chains. Longest chain 7 peptides. Score 0.256 Round 2: 138 peptides, 25 chains. Longest chain 10 peptides. Score 0.360 Round 3: 140 peptides, 26 chains. Longest chain 8 peptides. Score 0.350 Round 4: 150 peptides, 26 chains. Longest chain 11 peptides. Score 0.395 Round 5: 149 peptides, 26 chains. Longest chain 11 peptides. Score 0.391 Taking the results from Round 4 Chains 26, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 6109 restraints for refining 2572 atoms. 5639 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2785 (Rfree = 0.000) for 2572 atoms. Found 3 (12 requested) and removed 14 (6 requested) atoms. Cycle 17: After refmac, R = 0.2762 (Rfree = 0.000) for 2538 atoms. Found 0 (12 requested) and removed 10 (6 requested) atoms. Cycle 18: After refmac, R = 0.2746 (Rfree = 0.000) for 2528 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.2699 (Rfree = 0.000) for 2520 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 20: After refmac, R = 0.2622 (Rfree = 0.000) for 2516 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.91 4.60 Search for helices and strands: 0 residues in 0 chains, 2646 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2661 seeds are put forward Round 1: 119 peptides, 27 chains. Longest chain 8 peptides. Score 0.226 Round 2: 145 peptides, 28 chains. Longest chain 12 peptides. Score 0.334 Round 3: 137 peptides, 25 chains. Longest chain 11 peptides. Score 0.356 Round 4: 146 peptides, 26 chains. Longest chain 9 peptides. Score 0.377 Round 5: 150 peptides, 25 chains. Longest chain 15 peptides. Score 0.414 Taking the results from Round 5 Chains 25, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 6213 restraints for refining 2634 atoms. 5738 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2566 (Rfree = 0.000) for 2634 atoms. Found 5 (12 requested) and removed 12 (6 requested) atoms. Cycle 22: After refmac, R = 0.2516 (Rfree = 0.000) for 2617 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.2453 (Rfree = 0.000) for 2610 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.2434 (Rfree = 0.000) for 2605 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.2429 (Rfree = 0.000) for 2599 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.92 4.61 Search for helices and strands: 0 residues in 0 chains, 2730 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2749 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 7 peptides. Score 0.229 Round 2: 121 peptides, 22 chains. Longest chain 13 peptides. Score 0.341 Round 3: 120 peptides, 21 chains. Longest chain 11 peptides. Score 0.357 Round 4: 130 peptides, 23 chains. Longest chain 11 peptides. Score 0.363 Round 5: 137 peptides, 23 chains. Longest chain 9 peptides. Score 0.395 Taking the results from Round 5 Chains 23, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 6503 restraints for refining 2692 atoms. 6070 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2795 (Rfree = 0.000) for 2692 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 27: After refmac, R = 0.2725 (Rfree = 0.000) for 2681 atoms. Found 7 (12 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.2662 (Rfree = 0.000) for 2676 atoms. Found 1 (12 requested) and removed 9 (6 requested) atoms. Cycle 29: After refmac, R = 0.2587 (Rfree = 0.000) for 2666 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.2683 (Rfree = 0.000) for 2658 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.96 4.66 Search for helices and strands: 0 residues in 0 chains, 2762 seeds are put forward NCS extension: 0 residues added, 2762 seeds are put forward Round 1: 101 peptides, 22 chains. Longest chain 7 peptides. Score 0.239 Round 2: 114 peptides, 22 chains. Longest chain 9 peptides. Score 0.307 Round 3: 113 peptides, 21 chains. Longest chain 10 peptides. Score 0.323 Round 4: 104 peptides, 19 chains. Longest chain 9 peptides. Score 0.321 Round 5: 122 peptides, 19 chains. Longest chain 15 peptides. Score 0.407 Taking the results from Round 5 Chains 19, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 6726 restraints for refining 2745 atoms. 6333 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2751 (Rfree = 0.000) for 2745 atoms. Found 10 (13 requested) and removed 16 (6 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2583 (Rfree = 0.000) for 2726 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 33: After refmac, R = 0.2556 (Rfree = 0.000) for 2716 atoms. Found 0 (12 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.2540 (Rfree = 0.000) for 2706 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.2519 (Rfree = 0.000) for 2699 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.93 4.63 Search for helices and strands: 0 residues in 0 chains, 2818 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2834 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 7 peptides. Score 0.222 Round 2: 101 peptides, 18 chains. Longest chain 13 peptides. Score 0.328 Round 3: 95 peptides, 18 chains. Longest chain 13 peptides. Score 0.297 Round 4: 97 peptides, 17 chains. Longest chain 13 peptides. Score 0.330 Round 5: 92 peptides, 15 chains. Longest chain 13 peptides. Score 0.350 Taking the results from Round 5 Chains 15, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 6539 restraints for refining 2678 atoms. 6246 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2640 (Rfree = 0.000) for 2678 atoms. Found 11 (12 requested) and removed 9 (6 requested) atoms. Cycle 37: After refmac, R = 0.2566 (Rfree = 0.000) for 2678 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 38: After refmac, R = 0.2568 (Rfree = 0.000) for 2672 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 39: After refmac, R = 0.2544 (Rfree = 0.000) for 2670 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.2544 (Rfree = 0.000) for 2664 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.96 4.66 Search for helices and strands: 0 residues in 0 chains, 2781 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2800 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 8 peptides. Score 0.229 Round 2: 98 peptides, 19 chains. Longest chain 9 peptides. Score 0.291 Round 3: 91 peptides, 17 chains. Longest chain 8 peptides. Score 0.299 Round 4: 94 peptides, 18 chains. Longest chain 8 peptides. Score 0.292 Round 5: 91 peptides, 16 chains. Longest chain 10 peptides. Score 0.322 Taking the results from Round 5 Chains 16, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 6662 restraints for refining 2668 atoms. 6378 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2940 (Rfree = 0.000) for 2668 atoms. Found 7 (12 requested) and removed 10 (6 requested) atoms. Cycle 42: After refmac, R = 0.2730 (Rfree = 0.000) for 2664 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.2743 (Rfree = 0.000) for 2660 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.2691 (Rfree = 0.000) for 2654 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2673 (Rfree = 0.000) for 2650 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.96 4.66 Search for helices and strands: 0 residues in 0 chains, 2784 seeds are put forward NCS extension: 0 residues added, 2784 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 11 peptides. Score 0.276 Round 2: 94 peptides, 19 chains. Longest chain 9 peptides. Score 0.270 Round 3: 105 peptides, 19 chains. Longest chain 9 peptides. Score 0.326 Round 4: 91 peptides, 19 chains. Longest chain 8 peptides. Score 0.253 Round 5: 95 peptides, 16 chains. Longest chain 11 peptides. Score 0.342 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 79, 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 2itb-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3315 reflections ( 99.55 % complete ) and 6854 restraints for refining 2715 atoms. 6554 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2848 (Rfree = 0.000) for 2715 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2700 (Rfree = 0.000) for 2708 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2714 (Rfree = 0.000) for 2701 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2701 (Rfree = 0.000) for 2695 atoms. TimeTaking 28.73