Sun 23 Dec 22:22:49 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 2o08-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o08-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o08-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-3.4-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/2o08-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-3.4-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 22:22:58 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/2o08-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-3.4-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 376 and 0 Target number of residues in the AU: 376 Target solvent content: 0.6264 Checking the provided sequence file Detected sequence length: 188 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 376 Adjusted target solvent content: 0.63 Input MTZ file: 2o08-3.4-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: 20 Cell parameters: 87.690 166.470 74.630 90.000 90.000 90.000 Input sequence file: 2o08-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3008 target number of atoms Had to go as low as 0.90 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: 83.235 3.400 Wilson plot Bfac: 64.48 7673 reflections ( 98.01 % complete ) and 0 restraints for refining 3338 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3209 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3406 (Rfree = 0.000) for 3338 atoms. Found 25 (25 requested) and removed 27 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 3.10 Search for helices and strands: 0 residues in 0 chains, 3455 seeds are put forward NCS extension: 0 residues added, 3455 seeds are put forward Round 1: 185 peptides, 34 chains. Longest chain 16 peptides. Score 0.338 Round 2: 227 peptides, 32 chains. Longest chain 16 peptides. Score 0.487 Round 3: 224 peptides, 31 chains. Longest chain 25 peptides. Score 0.491 Round 4: 226 peptides, 26 chains. Longest chain 24 peptides. Score 0.555 Round 5: 226 peptides, 30 chains. Longest chain 20 peptides. Score 0.508 Taking the results from Round 4 Chains 29, Residues 200, Estimated correctness of the model 13.3 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5657 restraints for refining 2732 atoms. 4777 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2972 (Rfree = 0.000) for 2732 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 2: After refmac, R = 0.2857 (Rfree = 0.000) for 2671 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 3: After refmac, R = 0.2789 (Rfree = 0.000) for 2643 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 4: After refmac, R = 0.2543 (Rfree = 0.000) for 2621 atoms. Found 14 (20 requested) and removed 14 (10 requested) atoms. Cycle 5: After refmac, R = 0.2658 (Rfree = 0.000) for 2602 atoms. Found 15 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 2.97 Search for helices and strands: 0 residues in 0 chains, 2735 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2748 seeds are put forward Round 1: 217 peptides, 37 chains. Longest chain 16 peptides. Score 0.397 Round 2: 223 peptides, 33 chains. Longest chain 15 peptides. Score 0.464 Round 3: 252 peptides, 36 chains. Longest chain 19 peptides. Score 0.506 Round 4: 244 peptides, 30 chains. Longest chain 20 peptides. Score 0.554 Round 5: 229 peptides, 28 chains. Longest chain 18 peptides. Score 0.539 Taking the results from Round 4 Chains 32, Residues 214, Estimated correctness of the model 13.0 % 2 chains (34 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5495 restraints for refining 2735 atoms. 4516 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2833 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Cycle 7: After refmac, R = 0.2715 (Rfree = 0.000) for 2700 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 8: After refmac, R = 0.2512 (Rfree = 0.000) for 2676 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 9: After refmac, R = 0.2522 (Rfree = 0.000) for 2660 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. Cycle 10: After refmac, R = 0.2558 (Rfree = 0.000) for 2653 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 2.77 Search for helices and strands: 0 residues in 0 chains, 2777 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2790 seeds are put forward Round 1: 225 peptides, 36 chains. Longest chain 12 peptides. Score 0.433 Round 2: 237 peptides, 31 chains. Longest chain 27 peptides. Score 0.525 Round 3: 239 peptides, 30 chains. Longest chain 22 peptides. Score 0.541 Round 4: 241 peptides, 31 chains. Longest chain 21 peptides. Score 0.535 Round 5: 235 peptides, 30 chains. Longest chain 15 peptides. Score 0.531 Taking the results from Round 3 Chains 30, Residues 209, Estimated correctness of the model 8.3 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5778 restraints for refining 2735 atoms. 4915 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2881 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 45 (10 requested) atoms. Cycle 12: After refmac, R = 0.2791 (Rfree = 0.000) for 2695 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. Cycle 13: After refmac, R = 0.2820 (Rfree = 0.000) for 2677 atoms. Found 20 (20 requested) and removed 28 (10 requested) atoms. Cycle 14: After refmac, R = 0.2537 (Rfree = 0.000) for 2657 atoms. Found 17 (20 requested) and removed 21 (10 requested) atoms. Cycle 15: After refmac, R = 0.2480 (Rfree = 0.000) for 2640 atoms. Found 13 (20 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 2.90 Search for helices and strands: 0 residues in 0 chains, 2742 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2764 seeds are put forward Round 1: 196 peptides, 34 chains. Longest chain 11 peptides. Score 0.373 Round 2: 234 peptides, 27 chains. Longest chain 19 peptides. Score 0.563 Round 3: 221 peptides, 29 chains. Longest chain 16 peptides. Score 0.507 Round 4: 234 peptides, 28 chains. Longest chain 17 peptides. Score 0.552 Round 5: 225 peptides, 26 chains. Longest chain 16 peptides. Score 0.552 Taking the results from Round 2 Chains 28, Residues 207, Estimated correctness of the model 16.1 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5422 restraints for refining 2735 atoms. 4476 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2791 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 44 (10 requested) atoms. Cycle 17: After refmac, R = 0.2846 (Rfree = 0.000) for 2690 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. Cycle 18: After refmac, R = 0.2875 (Rfree = 0.000) for 2665 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 19: After refmac, R = 0.2800 (Rfree = 0.000) for 2649 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. Cycle 20: After refmac, R = 0.2895 (Rfree = 0.000) for 2641 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 2.79 Search for helices and strands: 0 residues in 0 chains, 2749 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2768 seeds are put forward Round 1: 209 peptides, 34 chains. Longest chain 14 peptides. Score 0.412 Round 2: 225 peptides, 36 chains. Longest chain 13 peptides. Score 0.433 Round 3: 215 peptides, 31 chains. Longest chain 15 peptides. Score 0.467 Round 4: 233 peptides, 34 chains. Longest chain 21 peptides. Score 0.479 Round 5: 219 peptides, 31 chains. Longest chain 21 peptides. Score 0.478 Taking the results from Round 4 Chains 34, Residues 199, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5818 restraints for refining 2735 atoms. 5025 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3052 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 22: After refmac, R = 0.3071 (Rfree = 0.000) for 2718 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 23: After refmac, R = 0.2979 (Rfree = 0.000) for 2710 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 24: After refmac, R = 0.2928 (Rfree = 0.000) for 2703 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 25: After refmac, R = 0.2822 (Rfree = 0.000) for 2702 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 2.99 Search for helices and strands: 0 residues in 0 chains, 2860 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2884 seeds are put forward Round 1: 194 peptides, 34 chains. Longest chain 16 peptides. Score 0.366 Round 2: 211 peptides, 31 chains. Longest chain 13 peptides. Score 0.456 Round 3: 194 peptides, 31 chains. Longest chain 12 peptides. Score 0.406 Round 4: 207 peptides, 29 chains. Longest chain 16 peptides. Score 0.469 Round 5: 220 peptides, 31 chains. Longest chain 17 peptides. Score 0.480 Taking the results from Round 5 Chains 31, Residues 189, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5886 restraints for refining 2735 atoms. 5161 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3219 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 27: After refmac, R = 0.3022 (Rfree = 0.000) for 2715 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 28: After refmac, R = 0.3035 (Rfree = 0.000) for 2688 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 29: After refmac, R = 0.3001 (Rfree = 0.000) for 2664 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Cycle 30: After refmac, R = 0.2863 (Rfree = 0.000) for 2651 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 2.86 Search for helices and strands: 0 residues in 0 chains, 2799 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 2817 seeds are put forward Round 1: 165 peptides, 32 chains. Longest chain 10 peptides. Score 0.301 Round 2: 206 peptides, 31 chains. Longest chain 14 peptides. Score 0.441 Round 3: 202 peptides, 29 chains. Longest chain 17 peptides. Score 0.455 Round 4: 197 peptides, 30 chains. Longest chain 15 peptides. Score 0.428 Round 5: 206 peptides, 29 chains. Longest chain 17 peptides. Score 0.467 Taking the results from Round 5 Chains 29, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 6035 restraints for refining 2735 atoms. 5356 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2920 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 32: After refmac, R = 0.2845 (Rfree = 0.000) for 2718 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 33: After refmac, R = 0.2897 (Rfree = 0.000) for 2703 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 34: After refmac, R = 0.2810 (Rfree = 0.000) for 2702 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 35: After refmac, R = 0.2774 (Rfree = 0.000) for 2704 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 2.83 Search for helices and strands: 0 residues in 0 chains, 2846 seeds are put forward NCS extension: 0 residues added, 2846 seeds are put forward Round 1: 177 peptides, 34 chains. Longest chain 9 peptides. Score 0.312 Round 2: 203 peptides, 31 chains. Longest chain 13 peptides. Score 0.433 Round 3: 193 peptides, 29 chains. Longest chain 17 peptides. Score 0.430 Round 4: 185 peptides, 31 chains. Longest chain 14 peptides. Score 0.379 Round 5: 185 peptides, 28 chains. Longest chain 18 peptides. Score 0.419 Taking the results from Round 2 Chains 31, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 6153 restraints for refining 2735 atoms. 5496 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2911 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 37: After refmac, R = 0.2846 (Rfree = 0.000) for 2720 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 38: After refmac, R = 0.2773 (Rfree = 0.000) for 2718 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2677 (Rfree = 0.000) for 2710 atoms. Found 20 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.2761 (Rfree = 0.000) for 2706 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 2.81 Search for helices and strands: 0 residues in 0 chains, 2860 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2881 seeds are put forward Round 1: 175 peptides, 32 chains. Longest chain 9 peptides. Score 0.334 Round 2: 194 peptides, 30 chains. Longest chain 18 peptides. Score 0.419 Round 3: 204 peptides, 31 chains. Longest chain 17 peptides. Score 0.436 Round 4: 192 peptides, 28 chains. Longest chain 19 peptides. Score 0.440 Round 5: 203 peptides, 28 chains. Longest chain 18 peptides. Score 0.471 Taking the results from Round 5 Chains 28, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 6132 restraints for refining 2735 atoms. 5460 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2884 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 42: After refmac, R = 0.2936 (Rfree = 0.000) for 2721 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 43: After refmac, R = 0.2610 (Rfree = 0.000) for 2705 atoms. Found 12 (20 requested) and removed 15 (10 requested) atoms. Cycle 44: After refmac, R = 0.2631 (Rfree = 0.000) for 2694 atoms. Found 12 (20 requested) and removed 12 (10 requested) atoms. Cycle 45: After refmac, R = 0.2896 (Rfree = 0.000) for 2692 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 2.86 Search for helices and strands: 0 residues in 0 chains, 2835 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 2855 seeds are put forward Round 1: 155 peptides, 28 chains. Longest chain 11 peptides. Score 0.325 Round 2: 182 peptides, 28 chains. Longest chain 16 peptides. Score 0.410 Round 3: 184 peptides, 28 chains. Longest chain 19 peptides. Score 0.416 Round 4: 202 peptides, 30 chains. Longest chain 22 peptides. Score 0.443 Round 5: 191 peptides, 26 chains. Longest chain 19 peptides. Score 0.463 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 165, 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 2o08-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7673 reflections ( 98.01 % complete ) and 6087 restraints for refining 2734 atoms. 5453 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2970 (Rfree = 0.000) for 2734 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.3007 (Rfree = 0.000) for 2708 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.3029 (Rfree = 0.000) for 2683 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.3042 (Rfree = 0.000) for 2664 atoms. TimeTaking 52.58