Sun 23 Dec 22:22:53 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 1zbt-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zbt-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zbt-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-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/1zbt-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-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 22:23:03 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/1zbt-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-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 338 and 0 Target number of residues in the AU: 338 Target solvent content: 0.6210 Checking the provided sequence file Detected sequence length: 371 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 371 Adjusted target solvent content: 0.58 Input MTZ file: 1zbt-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: 96 Cell parameters: 71.823 71.823 187.134 90.000 90.000 90.000 Input sequence file: 1zbt-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2968 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 Loops will be built when appropriate and at the last cycle Resolution range: 28.608 3.200 Wilson plot Bfac: 61.57 8652 reflections ( 99.77 % complete ) and 0 restraints for refining 3293 atoms. Observations/parameters ratio is 0.66 ------------------------------------------------------ Starting model: R = 0.3273 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3400 (Rfree = 0.000) for 3293 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 2.86 Search for helices and strands: 0 residues in 0 chains, 3360 seeds are put forward Round 1: 170 peptides, 20 chains. Longest chain 22 peptides. Score 0.509 Round 2: 186 peptides, 15 chains. Longest chain 52 peptides. Score 0.619 Round 3: 204 peptides, 19 chains. Longest chain 42 peptides. Score 0.615 Round 4: 209 peptides, 18 chains. Longest chain 31 peptides. Score 0.639 Round 5: 217 peptides, 18 chains. Longest chain 69 peptides. Score 0.657 Taking the results from Round 5 Chains 19, Residues 199, Estimated correctness of the model 55.5 % 2 chains (67 residues) have been docked in sequence ------------------------------------------------------ 8652 reflections ( 99.77 % complete ) and 5188 restraints for refining 2634 atoms. 4144 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3054 (Rfree = 0.000) for 2634 atoms. Found 23 (23 requested) and removed 32 (11 requested) atoms. Cycle 2: After refmac, R = 0.2917 (Rfree = 0.000) for 2555 atoms. Found 21 (23 requested) and removed 27 (11 requested) atoms. Cycle 3: After refmac, R = 0.2819 (Rfree = 0.000) for 2521 atoms. Found 17 (22 requested) and removed 26 (11 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2898 (Rfree = 0.000) for 2492 atoms. Found 20 (22 requested) and removed 24 (11 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2693 (Rfree = 0.000) for 2473 atoms. Found 13 (22 requested) and removed 23 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.16 2.84 Search for helices and strands: 0 residues in 0 chains, 2546 seeds are put forward Round 1: 209 peptides, 20 chains. Longest chain 49 peptides. Score 0.615 Round 2: 235 peptides, 17 chains. Longest chain 69 peptides. Score 0.706 Round 3: 235 peptides, 21 chains. Longest chain 54 peptides. Score 0.665 Round 4: 232 peptides, 17 chains. Longest chain 40 peptides. Score 0.700 Round 5: 238 peptides, 18 chains. Longest chain 41 peptides. Score 0.702 Taking the results from Round 2 Chains 21, Residues 218, Estimated correctness of the model 66.4 % 5 chains (116 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 166 A and 174 A Built loop between residues 304 A and 315 A 16 chains (229 residues) following loop building 3 chains (133 residues) in sequence following loop building ------------------------------------------------------ 8652 reflections ( 99.77 % complete ) and 3879 restraints for refining 2555 atoms. 2472 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2995 (Rfree = 0.000) for 2555 atoms. Found 22 (22 requested) and removed 42 (11 requested) atoms. Cycle 7: After refmac, R = 0.2922 (Rfree = 0.000) for 2513 atoms. Found 19 (22 requested) and removed 41 (11 requested) atoms. Cycle 8: After refmac, R = 0.2919 (Rfree = 0.000) for 2476 atoms. Found 16 (21 requested) and removed 31 (11 requested) atoms. Cycle 9: After refmac, R = 0.2913 (Rfree = 0.000) for 2431 atoms. Found 21 (21 requested) and removed 28 (11 requested) atoms. Cycle 10: After refmac, R = 0.2551 (Rfree = 0.000) for 2400 atoms. Found 10 (19 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 2.83 Search for helices and strands: 0 residues in 0 chains, 2482 seeds are put forward Round 1: 223 peptides, 23 chains. Longest chain 37 peptides. Score 0.615 Round 2: 232 peptides, 18 chains. Longest chain 71 peptides. Score 0.690 Round 3: 241 peptides, 21 chains. Longest chain 52 peptides. Score 0.678 Round 4: 234 peptides, 19 chains. Longest chain 41 peptides. Score 0.684 Round 5: 232 peptides, 20 chains. Longest chain 41 peptides. Score 0.669 Taking the results from Round 2 Chains 18, Residues 214, Estimated correctness of the model 63.0 % 3 chains (117 residues) have been docked in sequence ------------------------------------------------------ 8652 reflections ( 99.77 % complete ) and 4147 restraints for refining 2560 atoms. 2829 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2722 (Rfree = 0.000) for 2560 atoms. Found 17 (21 requested) and removed 31 (11 requested) atoms. Cycle 12: After refmac, R = 0.2666 (Rfree = 0.000) for 2533 atoms. Found 14 (20 requested) and removed 25 (11 requested) atoms. Cycle 13: After refmac, R = 0.2605 (Rfree = 0.000) for 2512 atoms. Found 14 (20 requested) and removed 20 (11 requested) atoms. Cycle 14: After refmac, R = 0.2588 (Rfree = 0.000) for 2498 atoms. Found 17 (20 requested) and removed 21 (11 requested) atoms. Cycle 15: After refmac, R = 0.2337 (Rfree = 0.000) for 2484 atoms. Found 16 (20 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 2.82 Search for helices and strands: 0 residues in 0 chains, 2555 seeds are put forward Round 1: 213 peptides, 24 chains. Longest chain 31 peptides. Score 0.577 Round 2: 229 peptides, 20 chains. Longest chain 51 peptides. Score 0.662 Round 3: 238 peptides, 21 chains. Longest chain 32 peptides. Score 0.671 Round 4: 232 peptides, 17 chains. Longest chain 51 peptides. Score 0.700 Round 5: 229 peptides, 19 chains. Longest chain 51 peptides. Score 0.673 Taking the results from Round 4 Chains 20, Residues 215, Estimated correctness of the model 65.2 % 5 chains (120 residues) have been docked in sequence ------------------------------------------------------ 8652 reflections ( 99.77 % complete ) and 4304 restraints for refining 2681 atoms. 2976 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2881 (Rfree = 0.000) for 2681 atoms. Found 22 (22 requested) and removed 62 (12 requested) atoms. Cycle 17: After refmac, R = 0.2767 (Rfree = 0.000) for 2626 atoms. Found 14 (21 requested) and removed 24 (11 requested) atoms. Cycle 18: After refmac, R = 0.2676 (Rfree = 0.000) for 2605 atoms. Found 21 (21 requested) and removed 26 (11 requested) atoms. Cycle 19: After refmac, R = 0.2689 (Rfree = 0.000) for 2593 atoms. Found 21 (21 requested) and removed 26 (11 requested) atoms. Cycle 20: After refmac, R = 0.2679 (Rfree = 0.000) for 2582 atoms. Found 21 (21 requested) and removed 30 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.10 2.78 Search for helices and strands: 0 residues in 0 chains, 2639 seeds are put forward Round 1: 216 peptides, 20 chains. Longest chain 45 peptides. Score 0.632 Round 2: 221 peptides, 18 chains. Longest chain 39 peptides. Score 0.666 Round 3: 213 peptides, 18 chains. Longest chain 47 peptides. Score 0.648 Round 4: 228 peptides, 17 chains. Longest chain 50 peptides. Score 0.692 Round 5: 222 peptides, 18 chains. Longest chain 29 peptides. Score 0.668 Taking the results from Round 4 Chains 17, Residues 211, Estimated correctness of the model 63.5 % 7 chains (141 residues) have been docked in sequence ------------------------------------------------------ 8652 reflections ( 99.77 % complete ) and 4256 restraints for refining 2708 atoms. 2866 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2754 (Rfree = 0.000) for 2708 atoms. Found 22 (22 requested) and removed 31 (12 requested) atoms. Cycle 22: After refmac, R = 0.2667 (Rfree = 0.000) for 2685 atoms. Found 22 (22 requested) and removed 29 (12 requested) atoms. Cycle 23: After refmac, R = 0.2748 (Rfree = 0.000) for 2660 atoms. Found 22 (22 requested) and removed 29 (12 requested) atoms. Cycle 24: After refmac, R = 0.2670 (Rfree = 0.000) for 2636 atoms. Found 20 (21 requested) and removed 20 (11 requested) atoms. Cycle 25: After refmac, R = 0.2664 (Rfree = 0.000) for 2615 atoms. Found 20 (21 requested) and removed 24 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 2.84 Search for helices and strands: 0 residues in 0 chains, 2698 seeds are put forward Round 1: 211 peptides, 20 chains. Longest chain 30 peptides. Score 0.620 Round 2: 215 peptides, 17 chains. Longest chain 59 peptides. Score 0.664 Round 3: 241 peptides, 20 chains. Longest chain 42 peptides. Score 0.688 Round 4: 220 peptides, 18 chains. Longest chain 29 peptides. Score 0.664 Round 5: 221 peptides, 19 chains. Longest chain 32 peptides. Score 0.655 Taking the results from Round 3 Chains 21, Residues 221, Estimated correctness of the model 62.6 % 6 chains (123 residues) have been docked in sequence ------------------------------------------------------ 8652 reflections ( 99.77 % complete ) and 4222 restraints for refining 2709 atoms. 2854 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2646 (Rfree = 0.000) for 2709 atoms. Found 20 (22 requested) and removed 45 (12 requested) atoms. Cycle 27: After refmac, R = 0.2741 (Rfree = 0.000) for 2670 atoms. Found 22 (22 requested) and removed 32 (12 requested) atoms. Cycle 28: After refmac, R = 0.2649 (Rfree = 0.000) for 2648 atoms. Found 21 (21 requested) and removed 30 (11 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2562 (Rfree = 0.000) for 2629 atoms. Found 21 (21 requested) and removed 26 (11 requested) atoms. Cycle 30: After refmac, R = 0.2171 (Rfree = 0.000) for 2616 atoms. Found 9 (21 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 2.83 Search for helices and strands: 0 residues in 0 chains, 2696 seeds are put forward Round 1: 206 peptides, 23 chains. Longest chain 42 peptides. Score 0.571 Round 2: 225 peptides, 18 chains. Longest chain 44 peptides. Score 0.675 Round 3: 217 peptides, 23 chains. Longest chain 39 peptides. Score 0.600 Round 4: 221 peptides, 20 chains. Longest chain 38 peptides. Score 0.644 Round 5: 215 peptides, 18 chains. Longest chain 36 peptides. Score 0.653 Taking the results from Round 2 Chains 20, Residues 207, Estimated correctness of the model 59.7 % 5 chains (116 residues) have been docked in sequence ------------------------------------------------------ 8652 reflections ( 99.77 % complete ) and 4380 restraints for refining 2709 atoms. 3061 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2803 (Rfree = 0.000) for 2709 atoms. Found 7 (22 requested) and removed 42 (12 requested) atoms. Cycle 32: After refmac, R = 0.2955 (Rfree = 0.000) for 2646 atoms. Found 21 (21 requested) and removed 30 (11 requested) atoms. Cycle 33: After refmac, R = 0.2785 (Rfree = 0.000) for 2619 atoms. Found 21 (21 requested) and removed 23 (11 requested) atoms. Cycle 34: After refmac, R = 0.2786 (Rfree = 0.000) for 2607 atoms. Found 21 (21 requested) and removed 19 (11 requested) atoms. Cycle 35: After refmac, R = 0.2405 (Rfree = 0.000) for 2595 atoms. Found 7 (21 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 2.85 Search for helices and strands: 0 residues in 0 chains, 2663 seeds are put forward Round 1: 199 peptides, 22 chains. Longest chain 24 peptides. Score 0.565 Round 2: 217 peptides, 19 chains. Longest chain 51 peptides. Score 0.646 Round 3: 217 peptides, 20 chains. Longest chain 33 peptides. Score 0.635 Round 4: 220 peptides, 22 chains. Longest chain 33 peptides. Score 0.619 Round 5: 226 peptides, 18 chains. Longest chain 31 peptides. Score 0.677 Taking the results from Round 5 Chains 18, Residues 208, Estimated correctness of the model 60.1 % 5 chains (117 residues) have been docked in sequence ------------------------------------------------------ 8652 reflections ( 99.77 % complete ) and 4303 restraints for refining 2708 atoms. 2991 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2921 (Rfree = 0.000) for 2708 atoms. Found 22 (22 requested) and removed 42 (12 requested) atoms. Cycle 37: After refmac, R = 0.2757 (Rfree = 0.000) for 2658 atoms. Found 22 (22 requested) and removed 24 (12 requested) atoms. Cycle 38: After refmac, R = 0.2677 (Rfree = 0.000) for 2642 atoms. Found 21 (21 requested) and removed 32 (11 requested) atoms. Cycle 39: After refmac, R = 0.2675 (Rfree = 0.000) for 2612 atoms. Found 21 (21 requested) and removed 26 (11 requested) atoms. Cycle 40: After refmac, R = 0.2695 (Rfree = 0.000) for 2595 atoms. Found 21 (21 requested) and removed 30 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 2.83 Search for helices and strands: 0 residues in 0 chains, 2679 seeds are put forward Round 1: 208 peptides, 20 chains. Longest chain 29 peptides. Score 0.613 Round 2: 218 peptides, 19 chains. Longest chain 56 peptides. Score 0.648 Round 3: 227 peptides, 21 chains. Longest chain 30 peptides. Score 0.647 Round 4: 224 peptides, 21 chains. Longest chain 41 peptides. Score 0.640 Round 5: 225 peptides, 18 chains. Longest chain 59 peptides. Score 0.675 Taking the results from Round 5 Chains 23, Residues 207, Estimated correctness of the model 59.7 % 8 chains (134 residues) have been docked in sequence ------------------------------------------------------ 8652 reflections ( 99.77 % complete ) and 4191 restraints for refining 2709 atoms. 2853 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2919 (Rfree = 0.000) for 2709 atoms. Found 21 (22 requested) and removed 40 (12 requested) atoms. Cycle 42: After refmac, R = 0.2752 (Rfree = 0.000) for 2675 atoms. Found 19 (22 requested) and removed 23 (12 requested) atoms. Cycle 43: After refmac, R = 0.2384 (Rfree = 0.000) for 2645 atoms. Found 16 (21 requested) and removed 19 (11 requested) atoms. Cycle 44: After refmac, R = 0.2201 (Rfree = 0.000) for 2635 atoms. Found 10 (21 requested) and removed 20 (11 requested) atoms. Cycle 45: After refmac, R = 0.2155 (Rfree = 0.000) for 2619 atoms. Found 6 (21 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 2.86 Search for helices and strands: 0 residues in 0 chains, 2696 seeds are put forward Round 1: 211 peptides, 26 chains. Longest chain 23 peptides. Score 0.547 Round 2: 224 peptides, 20 chains. Longest chain 51 peptides. Score 0.651 Round 3: 225 peptides, 19 chains. Longest chain 40 peptides. Score 0.664 Round 4: 225 peptides, 18 chains. Longest chain 40 peptides. Score 0.675 Round 5: 225 peptides, 21 chains. Longest chain 51 peptides. Score 0.642 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 207, Estimated correctness of the model 59.7 % 6 chains (136 residues) have been docked in sequence Sequence coverage is 65 % Consider running further cycles of model building using 1zbt-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 165 A and 175 A Built loop between residues 183 A and 186 A Built loop between residues 279 A and 282 A 16 chains (220 residues) following loop building 3 chains (149 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8652 reflections ( 99.77 % complete ) and 4018 restraints for refining 2709 atoms. 2553 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2700 (Rfree = 0.000) for 2709 atoms. Found 0 (22 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2667 (Rfree = 0.000) for 2679 atoms. Found 0 (22 requested) and removed 7 (12 requested) atoms. Cycle 48: After refmac, R = 0.2678 (Rfree = 0.000) for 2657 atoms. Found 0 (21 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2565 (Rfree = 0.000) for 2637 atoms. TimeTaking 52.78